diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 3626 |
1 files changed, 2310 insertions, 1316 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index cb3c4bc1fd..026527cd36 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11,6 +11,7 @@ ;;; Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net> ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com> ;;; Copyright © 2018 Gábor Boskovits <boskovits@gmail.com> +;;; Copyright © 2018 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> ;;; ;;; This file is part of GNU Guix. ;;; @@ -37,6 +38,7 @@ #:use-module (guix build-system ant) #:use-module (guix build-system gnu) #:use-module (guix build-system cmake) + #:use-module (guix build-system haskell) #:use-module (guix build-system ocaml) #:use-module (guix build-system perl) #:use-module (guix build-system python) @@ -50,6 +52,7 @@ #:use-module (gnu packages base) #:use-module (gnu packages bash) #:use-module (gnu packages bison) + #:use-module (gnu packages bioconductor) #:use-module (gnu packages boost) #:use-module (gnu packages check) #:use-module (gnu packages compression) @@ -70,11 +73,13 @@ #:use-module (gnu packages groff) #:use-module (gnu packages guile) #:use-module (gnu packages haskell) + #:use-module (gnu packages haskell-check) + #:use-module (gnu packages haskell-web) #:use-module (gnu packages image) #:use-module (gnu packages imagemagick) #:use-module (gnu packages java) #:use-module (gnu packages jemalloc) - #:use-module (gnu packages ldc) + #:use-module (gnu packages dlang) #:use-module (gnu packages linux) #:use-module (gnu packages logging) #:use-module (gnu packages machine-learning) @@ -131,24 +136,23 @@ (modify-phases %standard-phases (delete 'configure) (replace 'build - (lambda _ - (zero? (system* "gcc" - "-O3" - "-ffast-math" - "-finline-functions" - "-o" - "aragorn" - (string-append "aragorn" ,version ".c"))))) + (lambda _ + (invoke "gcc" + "-O3" + "-ffast-math" + "-finline-functions" + "-o" + "aragorn" + (string-append "aragorn" ,version ".c")) + #t)) (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (bin (string-append out "/bin")) - (man (string-append out "/share/man/man1"))) - (mkdir-p bin) - (install-file "aragorn" bin) - (mkdir-p man) - (install-file "aragorn.1" man)) - #t))))) + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin")) + (man (string-append out "/share/man/man1"))) + (install-file "aragorn" bin) + (install-file "aragorn.1" man)) + #t))))) (home-page "http://mbio-serv2.mbioekol.lu.se/ARAGORN") (synopsis "Detect tRNA, mtRNA and tmRNA genes in nucleotide sequences") (description @@ -163,15 +167,16 @@ structure of the predicted RNA.") (name "bamm") (version "1.7.3") (source (origin - (method url-fetch) + (method git-fetch) ;; BamM is not available on pypi. - (uri (string-append - "https://github.com/Ecogenomics/BamM/archive/" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (uri (git-reference + (url "https://github.com/Ecogenomics/BamM.git") + (commit version) + (recursive? #t))) + (file-name (git-file-name name version)) (sha256 (base32 - "1f35yxp4pc8aadsvbpg6r4kg2jh4fkjci0iby4iyljm6980sac0s")) + "1p83ahi984ipslxlg4yqy1gdnya9rkn1v71z8djgxkm9d2chw4c5")) (modules '((guix build utils))) (snippet `(begin @@ -193,11 +198,12 @@ structure of the predicted RNA.") (lambda _ (with-directory-excursion "c" (let ((sh (which "sh"))) + (for-each make-file-writable (find-files "." ".*")) ;; Use autogen so that 'configure' works. (substitute* "autogen.sh" (("/bin/sh") sh)) (setenv "CONFIG_SHELL" sh) - (substitute* "configure" (("/bin/sh") sh)) - (zero? (system* "./autogen.sh")))))) + (invoke "./autogen.sh"))) + #t)) (delete 'build) ;; Run tests after installation so compilation only happens once. (delete 'check) @@ -225,7 +231,8 @@ structure of the predicted RNA.") ;; There are 2 errors printed, but they are safe to ignore: ;; 1) [E::hts_open_format] fail to open file ... ;; 2) samtools view: failed to open ... - (zero? (system* "nosetests"))))))) + (invoke "nosetests") + #t))))) (native-inputs `(("autoconf" ,autoconf) ("automake" ,automake) @@ -255,14 +262,14 @@ instance, it implements several methods to assess contig-wise read coverage.") (name "bamtools") (version "2.5.1") (source (origin - (method url-fetch) - (uri (string-append - "https://github.com/pezmaster31/bamtools/archive/v" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/pezmaster31/bamtools.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "1z3kg24qrwq13a88n9d86izngrar4fll7gr6phddb2faw75pdgaa")))) + "0nfb2ypcx9959xnbz6wxh6py3xfizgmg8nrknxl95c507m9hmq8b")))) (build-system cmake-build-system) (arguments `(#:tests? #f ;no "check" target @@ -274,7 +281,8 @@ instance, it implements several methods to assess contig-wise read coverage.") (setenv "LDFLAGS" (string-append "-Wl,-rpath=" - (assoc-ref outputs "out") "/lib/bamtools"))))))) + (assoc-ref outputs "out") "/lib/bamtools")) + #t))))) (inputs `(("zlib" ,zlib))) (home-page "https://github.com/pezmaster31/bamtools") (synopsis "C++ API and command-line toolkit for working with BAM data") @@ -286,34 +294,25 @@ BAM files.") (define-public bcftools (package (name "bcftools") - (version "1.8") + (version "1.9") (source (origin (method url-fetch) - (uri (string-append - "https://github.com/samtools/bcftools/releases/download/" - version "/bcftools-" version ".tar.bz2")) + (uri (string-append "https://github.com/samtools/bcftools/" + "releases/download/" + version "/bcftools-" version ".tar.bz2")) (sha256 (base32 - "1vgw2mwngq20c530zim52zvgmw1lci8rzl33pvh44xqk3xlzvjsa")) + "1j3h638i8kgihzyrlnpj82xg1b23sijibys9hvwari3fy7kd0dkg")) (modules '((guix build utils))) (snippet '(begin ;; Delete bundled htslib. - (delete-file-recursively "htslib-1.8") + (delete-file-recursively "htslib-1.9") #t)))) (build-system gnu-build-system) (arguments - `(#:test-target "test" - #:configure-flags (list "--with-htslib=system") - #:make-flags - (list - "USE_GPL=1" - "LIBS=-lgsl -lgslcblas" - (string-append "prefix=" (assoc-ref %outputs "out")) - (string-append "HTSDIR=" (assoc-ref %build-inputs "htslib") "/include") - (string-append "HTSLIB=" (assoc-ref %build-inputs "htslib") "/lib/libhts.so") - (string-append "BGZIP=" (assoc-ref %build-inputs "htslib") "/bin/bgzip") - (string-append "TABIX=" (assoc-ref %build-inputs "htslib") "/bin/tabix") - (string-append "PACKAGE_VERSION=" ,version)) + `(#:configure-flags + (list "--enable-libgsl") + #:test-target "test" #:phases (modify-phases %standard-phases (add-before 'check 'patch-tests @@ -339,15 +338,16 @@ transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.") (define-public bedops (package (name "bedops") - (version "2.4.33") + (version "2.4.35") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/bedops/bedops/archive/v" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/bedops/bedops.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "0kx4awrwby8f33wqyx8w7ms7v25xhf0d421csgf96a3hfzn2mb0m")))) + "0mmgsgwz5r9w76hzgxkxc9s9lkdhhaf7vr6i02b09vbswvs1fyqx")))) (build-system gnu-build-system) (arguments '(#:tests? #f @@ -369,9 +369,9 @@ transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.") ;; Unpack the tarballs to benefit from shebang patching. (with-directory-excursion "third-party" - (and (zero? (system* "tar" "xvf" "jansson-2.6.tar.bz2")) - (zero? (system* "tar" "xvf" "zlib-1.2.7.tar.bz2")) - (zero? (system* "tar" "xvf" "bzip2-1.0.6.tar.bz2")))) + (invoke "tar" "xvf" "jansson-2.6.tar.bz2") + (invoke "tar" "xvf" "zlib-1.2.7.tar.bz2") + (invoke "tar" "xvf" "bzip2-1.0.6.tar.bz2")) ;; Disable unpacking of tarballs in Makefile. (substitute* "system.mk/Makefile.linux" (("^\tbzcat .*") "\t@echo \"not unpacking\"\n") @@ -439,11 +439,11 @@ BED, GFF/GTF, VCF.") (source (origin (method url-fetch) (uri (string-append "https://github.com/arq5x/bedtools2/" - "archive/v" version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + "releases/download/v" version + "/bedtools-" version ".tar.gz")) (sha256 (base32 - "05vrnr8yp7swfagshzpgqmzk1blnwnq8pq5pckzi1m26w98d63vf")))) + "11rvca19ncg03kxd0wzlfx5ws7r3nisd0z8s9j9n182d8ksp2pxz")))) (arguments '(#:test-target "test" #:phases @@ -457,6 +457,20 @@ BED, GFF/GTF, VCF.") (find-files "bin" ".*"))) #t))))))) +;; Needed for pybedtools. +(define-public bedtools-2.26 + (package (inherit bedtools) + (name "bedtools") + (version "2.26.0") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/arq5x/bedtools2/releases/" + "download/v" version "/" + "bedtools-" version ".tar.gz")) + (sha256 + (base32 + "0jhavwifnf7lmkb11h9y7dynr8d699h0rd2l52j1pfgircr2zwv5")))))) + (define-public ribotaper (package (name "ribotaper") @@ -483,7 +497,8 @@ BED, GFF/GTF, VCF.") '("create_annotations_files.bash" "create_metaplots.bash" "Ribotaper_ORF_find.sh" - "Ribotaper.sh")))))))) + "Ribotaper.sh"))) + #t))))) (inputs `(("bedtools" ,bedtools-2.18) ("samtools" ,samtools-0.1) @@ -507,13 +522,14 @@ provides the Ribotaper pipeline.") (version "0.2.2") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/ratschlab/RiboDiff/" - "archive/v" version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/ratschlab/RiboDiff.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "0wpbwmfv05wdjxv7ikm664f7s7p7cqr8jnw99zrda0q67rl50aaj")))) + "0x75nlp7qnmm64jasbi6l21f2cy99r2cjyl6b4hr8zf2bq22drnz")))) (build-system python-build-system) (arguments `(#:python ,python-2 @@ -550,12 +566,14 @@ independently with transcriptional regulation.") (name "bioawk") (version "1.0") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/lh3/bioawk/archive/v" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) - (sha256 - (base32 "1daizxsk17ahi9n58fj8vpgwyhzrzh54bzqhanjanp88kgrz7gjw")))) + (method git-fetch) + (uri (git-reference + (url "https://github.com/lh3/bioawk.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1pxc3zdnirxbf9a0az698hd8xdik7qkhypm7v6hn922x8y9qmspm")))) (build-system gnu-build-system) (inputs `(("zlib" ,zlib))) @@ -569,13 +587,14 @@ independently with transcriptional regulation.") (modify-phases %standard-phases (delete 'configure) ; There is no configure phase. (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (bin (string-append out "/bin")) - (man (string-append out "/share/man/man1"))) - (mkdir-p man) - (copy-file "awk.1" (string-append man "/bioawk.1")) - (install-file "bioawk" bin))))))) + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin")) + (man (string-append out "/share/man/man1"))) + (mkdir-p man) + (copy-file "awk.1" (string-append man "/bioawk.1")) + (install-file "bioawk" bin)) + #t))))) (home-page "https://github.com/lh3/bioawk") (synopsis "AWK with bioinformatics extensions") (description "Bioawk is an extension to Brian Kernighan's awk, adding the @@ -586,29 +605,54 @@ input/output delimiter. When the new functionality is not used, bioawk is intended to behave exactly the same as the original BWK awk.") (license license:x11))) -(define-public python2-pybedtools +(define-public python-pybedtools (package - (name "python2-pybedtools") - (version "0.6.9") + (name "python-pybedtools") + (version "0.7.10") (source (origin (method url-fetch) - (uri (string-append - "https://pypi.python.org/packages/source/p/pybedtools/pybedtools-" - version ".tar.gz")) + (uri (pypi-uri "pybedtools" version)) (sha256 (base32 - "1ldzdxw1p4y3g2ignmggsdypvqkcwqwzhdha4rbgpih048z5p4an")))) + "0l2b2wrnj85azfqgr0zwr60f7j58vlla1hcgxvr9rwikpl8j72ji")))) (build-system python-build-system) - (arguments `(#:python ,python-2)) ; no Python 3 support - (inputs - `(("python-matplotlib" ,python2-matplotlib))) + (arguments + `(#:phases + (modify-phases %standard-phases + ;; See https://github.com/daler/pybedtools/issues/261 + (add-after 'unpack 'disable-broken-tests + (lambda _ + ;; This test (pybedtools.test.test_scripts.test_venn_mpl) needs a + ;; graphical environment. + (substitute* "pybedtools/test/test_scripts.py" + (("def test_venn_mpl") + "def _do_not_test_venn_mpl")) + ;; Requires internet access. + (substitute* "pybedtools/test/test_helpers.py" + (("def test_chromsizes") + "def _do_not_test_chromsizes")) + ;; FIXME: these two fail for no good reason. + (substitute* "pybedtools/test/test1.py" + (("def test_issue_157") + "def _do_not_test_issue_157") + (("def test_to_dataframe") + "def _do_not_test_to_dataframe")) + #t))))) (propagated-inputs - `(("bedtools" ,bedtools) - ("samtools" ,samtools))) + ;; Tests don't pass with Bedtools 2.27.1. + ;; See https://github.com/daler/pybedtools/issues/260 + `(("bedtools" ,bedtools-2.26) + ("samtools" ,samtools) + ("python-matplotlib" ,python-matplotlib) + ("python-pysam" ,python-pysam) + ("python-pyyaml" ,python-pyyaml))) (native-inputs - `(("python-cython" ,python2-cython) - ("python-pyyaml" ,python2-pyyaml) - ("python-nose" ,python2-nose))) + `(("python-numpy" ,python-numpy) + ("python-pandas" ,python-pandas) + ("python-cython" ,python-cython) + ("python-nose" ,python-nose) + ("kentutils" ,kentutils) ; for bedGraphToBigWig + ("python-six" ,python-six))) (home-page "https://pythonhosted.org/pybedtools/") (synopsis "Python wrapper for BEDtools programs") (description @@ -618,55 +662,109 @@ pybedtools extends BEDTools by offering feature-level manipulations from with Python.") (license license:gpl2+))) +(define-public python2-pybedtools + (let ((pkg (package-with-python2 python-pybedtools))) + (package (inherit pkg) + (arguments + `(#:modules ((ice-9 ftw) + (srfi srfi-1) + (srfi srfi-26) + (guix build utils) + (guix build python-build-system)) + ;; See https://github.com/daler/pybedtools/issues/192 + ,@(substitute-keyword-arguments (package-arguments pkg) + ((#:phases phases) + `(modify-phases ,phases + (replace 'check + (lambda _ + (let ((cwd (getcwd))) + (setenv "PYTHONPATH" + (string-append cwd "/build/" + (find (cut string-prefix? "lib" <>) + (scandir (string-append cwd "/build"))) + ":" (getenv "PYTHONPATH")))) + ;; The tests need to be run from elsewhere... + (mkdir-p "/tmp/test") + (copy-recursively "pybedtools/test" "/tmp/test") + (with-directory-excursion "/tmp/test" + (invoke "nosetests" + ;; This test fails for unknown reasons + "--exclude=.*test_getting_example_beds")) + #t)))))))))) + (define-public python-biom-format (package - (name "python-biom-format") - (version "2.1.6") - (source - (origin - (method url-fetch) - ;; Use GitHub as source because PyPI distribution does not contain - ;; test data: https://github.com/biocore/biom-format/issues/693 - (uri (string-append "https://github.com/biocore/biom-format/archive/" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) - (sha256 - (base32 - "08cr7wpahk6zb31h4bs7jmzpvxcqv9s13xz40h6y2h656jvdvnpj")))) - (build-system python-build-system) - (propagated-inputs - `(("python-numpy" ,python-numpy) - ("python-scipy" ,python-scipy) - ("python-future" ,python-future) - ("python-click" ,python-click) - ("python-h5py" ,python-h5py) - ("python-pandas" ,python-pandas))) - (native-inputs - `(("python-nose" ,python-nose))) - (home-page "http://www.biom-format.org") - (synopsis "Biological Observation Matrix (BIOM) format utilities") - (description - "The BIOM file format is designed to be a general-use format for + (name "python-biom-format") + (version "2.1.7") + (source + (origin + (method git-fetch) + ;; Use GitHub as source because PyPI distribution does not contain + ;; test data: https://github.com/biocore/biom-format/issues/693 + (uri (git-reference + (url "https://github.com/biocore/biom-format.git") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1rna16lyk5aqhnv0dp77wwaplias93f1vw28ad3jmyw6hwkai05v")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'use-cython + (lambda _ (setenv "USE_CYTHON" "1") #t)) + (add-after 'unpack 'disable-broken-test + (lambda _ + (substitute* "biom/tests/test_cli/test_validate_table.py" + (("^(.+)def test_invalid_hdf5" m indent) + (string-append indent + "@npt.dec.skipif(True, msg='Guix')\n" + m))) + #t)) + (add-before 'reset-gzip-timestamps 'make-files-writable + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (for-each (lambda (file) (chmod file #o644)) + (find-files out "\\.gz")) + #t)))))) + (propagated-inputs + `(("python-numpy" ,python-numpy) + ("python-scipy" ,python-scipy) + ("python-flake8" ,python-flake8) + ("python-future" ,python-future) + ("python-click" ,python-click) + ("python-h5py" ,python-h5py) + ("python-pandas" ,python-pandas))) + (native-inputs + `(("python-cython" ,python-cython) + ("python-pytest" ,python-pytest) + ("python-pytest-cov" ,python-pytest-cov) + ("python-nose" ,python-nose))) + (home-page "http://www.biom-format.org") + (synopsis "Biological Observation Matrix (BIOM) format utilities") + (description + "The BIOM file format is designed to be a general-use format for representing counts of observations e.g. operational taxonomic units, KEGG orthology groups or lipid types, in one or more biological samples e.g. microbiome samples, genomes, metagenomes.") - (license license:bsd-3) - (properties `((python2-variant . ,(delay python2-biom-format)))))) + (license license:bsd-3) + (properties `((python2-variant . ,(delay python2-biom-format)))))) (define-public python2-biom-format (let ((base (package-with-python2 (strip-python2-variant python-biom-format)))) (package (inherit base) (arguments - `(#:phases - (modify-phases %standard-phases - ;; Do not require the unmaintained pyqi library. - (add-after 'unpack 'remove-pyqi - (lambda _ - (substitute* "setup.py" - (("install_requires.append\\(\"pyqi\"\\)") "pass")) - #t))) - ,@(package-arguments base)))))) + (substitute-keyword-arguments (package-arguments base) + ((#:phases phases) + `(modify-phases ,phases + ;; Do not require the unmaintained pyqi library. + (add-after 'unpack 'remove-pyqi + (lambda _ + (substitute* "setup.py" + (("install_requires.append\\(\"pyqi\"\\)") "pass")) + #t))))))))) (define-public bioperl-minimal (let* ((inputs `(("perl-module-build" ,perl-module-build) @@ -1003,15 +1101,12 @@ package provides command line tools using the Bio++ library.") #:parallel-build? #f ; not supported #:phases (modify-phases %standard-phases - (add-before - 'configure 'set-HOME + (add-before 'configure 'set-HOME ;; $HOME needs to be set at some point during the configure phase (lambda _ (setenv "HOME" "/tmp") #t)) - (add-after - 'unpack 'enter-dir + (add-after 'unpack 'enter-dir (lambda _ (chdir "c++") #t)) - (add-after - 'enter-dir 'fix-build-system + (add-after 'enter-dir 'fix-build-system (lambda _ (define (which* cmd) (cond ((string=? cmd "date") @@ -1059,31 +1154,31 @@ package provides command line tools using the Bio++ library.") (("action=/bin/") "action=") (("export PATH") ":")) #t)) - (replace - 'configure - (lambda* (#:key inputs outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out")) - (lib (string-append (assoc-ref outputs "lib") "/lib")) - (include (string-append (assoc-ref outputs "include") - "/include/ncbi-tools++"))) - ;; The 'configure' script doesn't recognize things like - ;; '--enable-fast-install'. - (zero? (system* "./configure.orig" - (string-append "--with-build-root=" (getcwd) "/build") - (string-append "--prefix=" out) - (string-append "--libdir=" lib) - (string-append "--includedir=" include) - (string-append "--with-bz2=" - (assoc-ref inputs "bzip2")) - (string-append "--with-z=" - (assoc-ref inputs "zlib")) - (string-append "--with-pcre=" - (assoc-ref inputs "pcre")) - ;; Each library is built twice by default, once - ;; with "-static" in its name, and again - ;; without. - "--without-static" - "--with-dll")))))))) + (replace 'configure + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out")) + (lib (string-append (assoc-ref outputs "lib") "/lib")) + (include (string-append (assoc-ref outputs "include") + "/include/ncbi-tools++"))) + ;; The 'configure' script doesn't recognize things like + ;; '--enable-fast-install'. + (invoke "./configure.orig" + (string-append "--with-build-root=" (getcwd) "/build") + (string-append "--prefix=" out) + (string-append "--libdir=" lib) + (string-append "--includedir=" include) + (string-append "--with-bz2=" + (assoc-ref inputs "bzip2")) + (string-append "--with-z=" + (assoc-ref inputs "zlib")) + (string-append "--with-pcre=" + (assoc-ref inputs "pcre")) + ;; Each library is built twice by default, once + ;; with "-static" in its name, and again + ;; without. + "--without-static" + "--with-dll") + #t)))))) (outputs '("out" ; 21 MB "lib" ; 226 MB "include")) ; 33 MB @@ -1148,7 +1243,7 @@ confidence to have in an alignment.") '(#:tests? #f ;no "check" target #:make-flags (list (string-append "ZLIB=" - (assoc-ref %build-inputs "zlib") + (assoc-ref %build-inputs "zlib:static") "/lib/libz.a") (string-append "LDFLAGS=" (string-join '("-lboost_filesystem" @@ -1191,6 +1286,7 @@ confidence to have in an alignment.") ("boost" ,boost) ("sparsehash" ,sparsehash) ("pigz" ,pigz) + ("zlib:static" ,zlib "static") ("zlib" ,zlib))) (supported-systems '("x86_64-linux")) (home-page "https://sourceforge.net/p/bless-ec/wiki/Home/") @@ -1208,15 +1304,16 @@ errors at the end of reads.") (define-public bowtie (package (name "bowtie") - (version "2.3.2") + (version "2.3.4.3") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/BenLangmead/bowtie2/archive/v" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/BenLangmead/bowtie2.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "0hwa5r9qbglppb7sz5z79rlmmddr3n51n468jb3wh8rwjgn3yr90")) + "1zl3cf327y2p7p03cavymbh7b00djc7lncfaqih33n96iy9q8ibp")) (modules '((guix build utils))) (snippet '(begin @@ -1226,14 +1323,6 @@ errors at the end of reads.") (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\"")) #t)))) (build-system gnu-build-system) - (inputs - `(("perl" ,perl) - ("perl-clone" ,perl-clone) - ("perl-test-deep" ,perl-test-deep) - ("perl-test-simple" ,perl-test-simple) - ("python" ,python-2) - ("tbb" ,tbb) - ("zlib" ,zlib))) (arguments '(#:make-flags (list "allall" @@ -1243,11 +1332,21 @@ errors at the end of reads.") (modify-phases %standard-phases (delete 'configure) (replace 'check - (lambda* (#:key outputs #:allow-other-keys) - (zero? (system* "perl" - "scripts/test/simple_tests.pl" - "--bowtie2=./bowtie2" - "--bowtie2-build=./bowtie2-build"))))))) + (lambda _ + (invoke "perl" + "scripts/test/simple_tests.pl" + "--bowtie2=./bowtie2" + "--bowtie2-build=./bowtie2-build") + #t))))) + (inputs + `(("tbb" ,tbb) + ("zlib" ,zlib) + ("python" ,python-wrapper))) + (native-inputs + `(("perl" ,perl) + ("perl-clone" ,perl-clone) + ("perl-test-deep" ,perl-test-deep) + ("perl-test-simple" ,perl-test-simple))) (home-page "http://bowtie-bio.sourceforge.net/bowtie2/index.shtml") (synopsis "Fast and sensitive nucleotide sequence read aligner") (description @@ -1264,7 +1363,7 @@ gapped, local, and paired-end alignment modes.") (define-public tophat (package (name "tophat") - (version "2.1.0") + (version "2.1.1") (source (origin (method url-fetch) (uri (string-append @@ -1272,13 +1371,12 @@ gapped, local, and paired-end alignment modes.") version ".tar.gz")) (sha256 (base32 - "168zlzykq622zbgkh90a90f1bdgsxkscq2zxzbj8brq80hbjpyp7")) - (patches (search-patches "tophat-build-with-later-seqan.patch")) + "19add02kv2xhd6ihd779dr7x35ggym3jqr0m5c4315i1yfb0p11p")) (modules '((guix build utils))) (snippet '(begin ;; Remove bundled SeqAn and samtools - (delete-file-recursively "src/SeqAn-1.3") + (delete-file-recursively "src/SeqAn-1.4.2") (delete-file-recursively "src/samtools-0.1.18") #t)))) (build-system gnu-build-system) @@ -1315,7 +1413,7 @@ gapped, local, and paired-end alignment modes.") ("python" ,python-2) ("perl" ,perl) ("zlib" ,zlib) - ("seqan" ,seqan))) + ("seqan" ,seqan-1))) (home-page "http://ccb.jhu.edu/software/tophat/index.shtml") (synopsis "Spliced read mapper for RNA-Seq data") (description @@ -1382,13 +1480,14 @@ and more accurate. BWA-MEM also has better performance than BWA-backtrack for (name "bwa-pssm") (version "0.5.11") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/pkerpedjiev/bwa-pssm/" - "archive/" version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/pkerpedjiev/bwa-pssm.git") + (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 - "02p7mpbs4mlxmn84g2x4ghak638vbj4lqix2ipx5g84pz9bhdavg")))) + "076c4q0cdqz8jgylb067y9zmvxglppnzi3qiscn0xiypgc6lgb5r")))) (build-system gnu-build-system) (inputs `(("gdsl" ,gdsl) @@ -1406,54 +1505,52 @@ the original BWA alignment program and shares the genome index structure as well as many of the command line options.") (license license:gpl3+))) -(define-public python2-bx-python +(define-public python-bx-python (package - (name "python2-bx-python") - (version "0.7.3") + (name "python-bx-python") + (version "0.8.2") (source (origin (method url-fetch) (uri (pypi-uri "bx-python" version)) (sha256 (base32 - "15z2w3bvnc0n4qmb9bd6d8ylc2h2nj883x2w9iixf4x3vki9b22i")) - (modules '((guix build utils))) - (snippet - '(begin - (substitute* "setup.py" - ;; remove dependency on outdated "distribute" module - (("^from distribute_setup import use_setuptools") "") - (("^use_setuptools\\(\\)") "")) - #t)))) + "11kksg2rbzihpmcid823xvg42xi88m7sz58rzk29abybkxy0rszs")))) (build-system python-build-system) - (arguments - `(#:tests? #f ;tests fail because test data are not included - #:python ,python-2)) + ;; Tests fail because test data are not included + (arguments '(#:tests? #f)) + (propagated-inputs + `(("python-numpy" ,python-numpy) + ("python-six" ,python-six))) (inputs - `(("python-numpy" ,python2-numpy) - ("zlib" ,zlib))) + `(("zlib" ,zlib))) (native-inputs - `(("python-nose" ,python2-nose))) - (home-page "http://bitbucket.org/james_taylor/bx-python/") + `(("python-lzo" ,python-lzo) + ("python-nose" ,python-nose) + ("python-cython" ,python-cython))) + (home-page "https://github.com/bxlab/bx-python") (synopsis "Tools for manipulating biological data") (description "bx-python provides tools for manipulating biological data, particularly multiple sequence alignments.") (license license:expat))) +(define-public python2-bx-python + (package-with-python2 python-bx-python)) + (define-public python-pysam (package (name "python-pysam") - (version "0.13.0") + (version "0.15.1") (source (origin - (method url-fetch) + (method git-fetch) ;; Test data is missing on PyPi. - (uri (string-append - "https://github.com/pysam-developers/pysam/archive/v" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (uri (git-reference + (url "https://github.com/pysam-developers/pysam.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "0dzap2axin9cbbl0d825w294bpn00zagfm1sigamm4v2pm5bj9lp")) + "1vj367w6xbn9bpmksm162l1aipf7cj97h1q83y7jcpm33ihwpf7x")) (modules '((guix build utils))) (snippet '(begin ;; Drop bundled htslib. TODO: Also remove samtools @@ -1480,6 +1577,11 @@ multiple sequence alignments.") #t)) (replace 'check (lambda* (#:key inputs outputs #:allow-other-keys) + ;; This file contains tests that require a connection to the + ;; internet. + (delete-file "tests/tabix_test.py") + ;; FIXME: This test fails + (delete-file "tests/AlignmentFile_test.py") ;; Add first subdirectory of "build" directory to PYTHONPATH. (setenv "PYTHONPATH" (string-append @@ -1490,28 +1592,26 @@ multiple sequence alignments.") ;; Step out of source dir so python does not import from CWD. (with-directory-excursion "tests" (setenv "HOME" "/tmp") - (and (zero? (system* "make" "-C" "pysam_data")) - (zero? (system* "make" "-C" "cbcf_data")) - ;; Running nosetests without explicitly asking for a - ;; single process leads to a crash. Running with multiple - ;; processes fails because the tests are not designed to - ;; run in parallel. - - ;; FIXME: tests keep timing out on some systems. - ;; (zero? (system* "nosetests" "-v" - ;; "--processes" "1")) - ))))))) - (propagated-inputs - `(("htslib" ,htslib))) ; Included from installed header files. + (invoke "make" "-C" "pysam_data") + (invoke "make" "-C" "cbcf_data") + ;; Running nosetests without explicitly asking for a single + ;; process leads to a crash. Running with multiple processes + ;; fails because the tests are not designed to run in parallel. + + ;; FIXME: tests keep timing out on some systems. + (invoke "nosetests" "-v" "--processes" "1"))))))) + (propagated-inputs + `(("htslib" ,htslib))) ; Included from installed header files. (inputs - `(("ncurses" ,ncurses) - ("zlib" ,zlib))) + `(("ncurses" ,ncurses) + ("curl" ,curl) + ("zlib" ,zlib))) (native-inputs - `(("python-cython" ,python-cython) + `(("python-cython" ,python-cython) ;; Dependencies below are are for tests only. - ("samtools" ,samtools) - ("bcftools" ,bcftools) - ("python-nose" ,python-nose))) + ("samtools" ,samtools) + ("bcftools" ,bcftools) + ("python-nose" ,python-nose))) (home-page "https://github.com/pysam-developers/pysam") (synopsis "Python bindings to the SAMtools C API") (description @@ -1526,19 +1626,19 @@ also includes an interface for tabix.") (define-public python-twobitreader (package (name "python-twobitreader") - (version "3.1.4") + (version "3.1.6") (source (origin - (method url-fetch) - (uri (pypi-uri "twobitreader" version)) + (method git-fetch) + (uri (git-reference + (url "https://github.com/benjschiller/twobitreader") + (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 - "1q8wnj2kga9nz1lwc4w7qv52smfm536hp6mc8w6s53lhyj0mpi22")))) + "1qbxvv1h58cismbk1anpjrkpghsaiy64a11ir3lhy6qch6xf8n62")))) (build-system python-build-system) - (arguments - '(;; Tests are not distributed in the PyPi release. - ;; TODO Try building from the Git repo or asking the upstream maintainer - ;; to distribute the tests on PyPi. - #:tests? #f)) + ;; Tests are not included + (arguments '(#:tests? #f)) (native-inputs `(("python-sphinx" ,python-sphinx))) (home-page "https://github.com/benjschiller/twobitreader") @@ -1639,29 +1739,35 @@ databases.") (define-public clipper (package (name "clipper") - (version "1.1") + (version "1.2.1") (source (origin - (method url-fetch) - (uri (string-append - "https://github.com/YeoLab/clipper/archive/" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/YeoLab/clipper.git") + (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 - "0pflmsvhbf8izbgwhbhj1i7349sw1f55qpqj8ljmapp16hb0p0qi")) + "0fja1rj84wp9vpj8rxpj3n8zqzcqq454m904yp9as1w4phccirjb")) (modules '((guix build utils))) (snippet '(begin ;; remove unnecessary setup dependency (substitute* "setup.py" (("setup_requires = .*") "")) - (for-each delete-file - '("clipper/src/peaks.so" - "clipper/src/readsToWiggle.so")) - (delete-file-recursively "dist/") #t)))) (build-system python-build-system) - (arguments `(#:python ,python-2)) ; only Python 2 is supported + (arguments + `(#:python ,python-2 ; only Python 2 is supported + #:phases + (modify-phases %standard-phases + ;; This is fixed in upstream commit + ;; f6c2990198f906bf97730d95695b4bd5a6d01ddb. + (add-after 'unpack 'fix-typo + (lambda _ + (substitute* "clipper/src/readsToWiggle.pyx" + (("^sc.*") "")) + #t))))) (inputs `(("htseq" ,python2-htseq) ("python-pybedtools" ,python2-pybedtools) @@ -1709,7 +1815,8 @@ databases.") (copy-recursively "QuarryFiles" (string-append out "/QuarryFiles")) (install-file "CodingQuarry" bin) - (install-file "CufflinksGTF_to_CodingQuarryGFF3.py" bin))))))) + (install-file "CufflinksGTF_to_CodingQuarryGFF3.py" bin)) + #t))))) (inputs `(("openmpi" ,openmpi))) (native-search-paths (list (search-path-specification @@ -1819,31 +1926,18 @@ time.") (define-public crossmap (package (name "crossmap") - (version "0.2.1") + (version "0.2.9") (source (origin (method url-fetch) - (uri (string-append "mirror://sourceforge/crossmap/CrossMap-" - version ".tar.gz")) + (uri (pypi-uri "CrossMap" version)) (sha256 (base32 - "07y179f63d7qnzdvkqcziwk9bs3k4zhp81q392fp1hwszjdvy22f")) - ;; This patch has been sent upstream already and is available - ;; for download from Sourceforge, but it has not been merged. - (patches (search-patches "crossmap-allow-system-pysam.patch")) - (modules '((guix build utils))) - (snippet '(begin - ;; remove bundled copy of pysam - (delete-file-recursively "lib/pysam") - #t)))) + "1byhclrqnqpvc1rqkfh4jwj6yhn0x9y7jk47i0qcjlhk0pjkw92p")))) (build-system python-build-system) - (arguments - `(#:python ,python-2 - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'set-env - (lambda _ (setenv "CROSSMAP_USE_SYSTEM_PYSAM" "1") #t))))) + (arguments `(#:python ,python-2)) (inputs - `(("python-numpy" ,python2-numpy) + `(("python-bx-python" ,python2-bx-python) + ("python-numpy" ,python2-numpy) ("python-pysam" ,python2-pysam) ("zlib" ,zlib))) (native-inputs @@ -1857,22 +1951,46 @@ files between different genome assemblies. It supports most commonly used file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.") (license license:gpl2+))) +(define-public python-dnaio + (package + (name "python-dnaio") + (version "0.3") + (source + (origin + (method url-fetch) + (uri (pypi-uri "dnaio" version)) + (sha256 + (base32 + "0f16m7hdlm0fz1n7y5asy0v9ghyrq17ni1p9iybq22ddzyd49r27")))) + (build-system python-build-system) + (native-inputs + `(("python-cython" ,python-cython) + ("python-pytest" ,python-pytest) + ("python-xopen" ,python-xopen))) + (home-page "https://github.com/marcelm/dnaio/") + (synopsis "Read FASTA and FASTQ files efficiently") + (description + "dnaio is a Python library for fast parsing of FASTQ and also FASTA +files. The code was previously part of the cutadapt tool.") + (license license:expat))) + (define-public cutadapt (package (name "cutadapt") - (version "1.16") + (version "1.18") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/marcelm/cutadapt.git") (commit (string-append "v" version)))) - (file-name (string-append name "-" version "-checkout")) + (file-name (git-file-name name version)) (sha256 (base32 - "09pr02067jiks19nc0aby4xp70hhgvb554i2y1c04rv1m401w7q8")))) + "08bbfwyc0kvcd95jf2s95xiv9s3cbsxm39ydl0qck3fw3cviwxpg")))) (build-system python-build-system) (inputs - `(("python-xopen" ,python-xopen))) + `(("python-dnaio" ,python-dnaio) + ("python-xopen" ,python-xopen))) (native-inputs `(("python-cython" ,python-cython) ("python-pytest" ,python-pytest))) @@ -1886,42 +2004,33 @@ other types of unwanted sequence from high-throughput sequencing reads.") (define-public libbigwig (package (name "libbigwig") - (version "0.1.4") + (version "0.4.2") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/dpryan79/libBigWig/" - "archive/" version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/dpryan79/libBigWig.git") + (commit version))) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "098rjh35pi4a9q83n8wiwvyzykjqj6l8q189p1xgfw4ghywdlvw1")))) + "0h2smg24v5srdcqzrmz2g23cmlp4va465mgx8r2z571sfz8pv454")))) (build-system gnu-build-system) (arguments `(#:test-target "test" + #:tests? #f ; tests require access to the web #:make-flags (list "CC=gcc" (string-append "prefix=" (assoc-ref %outputs "out"))) #:phases (modify-phases %standard-phases - (delete 'configure) - (add-before 'check 'disable-curl-test - (lambda _ - (substitute* "Makefile" - (("./test/testRemote.*") "")) - #t)) - ;; This has been fixed with the upstream commit 4ff6959cd8a0, but - ;; there has not yet been a release containing this change. - (add-before 'install 'create-target-dirs - (lambda* (#:key outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out"))) - (mkdir-p (string-append out "/lib")) - (mkdir-p (string-append out "/include")) - #t)))))) + (delete 'configure)))) (inputs `(("zlib" ,zlib) ("curl" ,curl))) (native-inputs - `(("doxygen" ,doxygen))) + `(("doxygen" ,doxygen) + ;; Need for tests + ("python" ,python-2))) (home-page "https://github.com/dpryan79/libBigWig") (synopsis "C library for handling bigWig files") (description @@ -1932,13 +2041,13 @@ files.") (define-public python-pybigwig (package (name "python-pybigwig") - (version "0.2.5") + (version "0.3.12") (source (origin (method url-fetch) (uri (pypi-uri "pyBigWig" version)) (sha256 (base32 - "0yrpdxg3y0sny25x4w22lv1k47jzccqjmg7j4bp0hywklvp0hg7d")) + "00w4kfnm2c5l7wdwr2nj1z5djv8kzgf7h1zhsgv6njff1rwr26g0")) (modules '((guix build utils))) (snippet '(begin @@ -1954,6 +2063,8 @@ files.") (substitute* "setup.py" (("libs=\\[") "libs=[\"BigWig\", ")) #t))))) + (propagated-inputs + `(("python-numpy" ,python-numpy))) (inputs `(("libbigwig" ,libbigwig) ("zlib" ,zlib) @@ -1974,15 +2085,15 @@ accessing bigWig files.") (version "4.4.0") (source (origin - (method url-fetch) + (method git-fetch) ;; Source from GitHub so that tests are included. - (uri - (string-append "https://github.com/jeetsukumaran/DendroPy/archive/v" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (uri (git-reference + (url "https://github.com/jeetsukumaran/DendroPy.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "0v2fccny5xjaah546bsch1mw4kh61qq5frz2ibllxs9mp6ih9bsn")))) + "097hfyv2kaf4x92i4rjx0paw2cncxap48qivv8zxng4z7nhid0x9")))) (build-system python-build-system) (home-page "http://packages.python.org/DendroPy/") (synopsis "Library for phylogenetics and phylogenetic computing") @@ -1993,19 +2104,33 @@ trees (phylogenies) and characters.") (license license:bsd-3))) (define-public python2-dendropy - (package-with-python2 python-dendropy)) + (let ((base (package-with-python2 python-dendropy))) + (package + (inherit base) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'remove-failing-test + (lambda _ + ;; This test fails when the full test suite is run, as documented + ;; at https://github.com/jeetsukumaran/DendroPy/issues/74 + (substitute* "tests/test_dataio_nexml_reader_tree_list.py" + (("test_collection_comments_and_annotations") + "do_not_test_collection_comments_and_annotations")) + #t))) + ,@(package-arguments base)))))) (define-public python-py2bit (package (name "python-py2bit") - (version "0.2.1") + (version "0.3.0") (source (origin (method url-fetch) (uri (pypi-uri "py2bit" version)) (sha256 (base32 - "1cdf4qlmgwsh1f4k0wdv2sr8x9qn4366p0k3614vbd0fpqiarxrl")))) + "1vw2nvw1yrl7ikkqsqs1pg239yr5nspvd969r1x9arms1k25a1a5")))) (build-system python-build-system) (home-page "https://github.com/dpryan79/py2bit") (synopsis "Access 2bit files using lib2bit") @@ -2017,18 +2142,25 @@ with Python.") (define-public deeptools (package (name "deeptools") - (version "2.5.1") + (version "3.1.3") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/deeptools/deepTools/" - "archive/" version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/deeptools/deepTools.git") + (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 - "1q8i12l2gvk4n2s8lhyzwhh9g4qbc8lrk5l7maz00yvd5g6z5540")))) + "1vggnf52g6q2vifdl4cyi7s2fnfqq0ky2zrkj5zv2qfzsc3p3siw")))) (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + ;; This phase fails, but it's not needed. + (delete 'reset-gzip-timestamps)))) (inputs - `(("python-scipy" ,python-scipy) + `(("python-plotly" ,python-plotly) + ("python-scipy" ,python-scipy) ("python-numpy" ,python-numpy) ("python-numpydoc" ,python-numpydoc) ("python-matplotlib" ,python-matplotlib) @@ -2055,42 +2187,42 @@ identify enrichments with functional annotations of the genome.") (define-public delly (package (name "delly") - (version "0.7.7") + (version "0.7.9") (source (origin - (method url-fetch) - (uri (string-append - "https://github.com/tobiasrausch/delly/archive/v" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/dellytools/delly.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 - (base32 "0dkwy3pyxmi6dhh1lpsr3698ri5sslw9qz67hfys0bz8dgrqwabj")) - (patches (search-patches "delly-use-system-libraries.patch")))) + (base32 "034jqsxswy9gqdh2zkgc1js99qkv75ks4xvzgmh0284sraagv61z")) + (modules '((guix build utils))) + (snippet + '(begin + (delete-file-recursively "src/htslib") + #t)))) (build-system gnu-build-system) (arguments `(#:tests? #f ; There are no tests to run. - #:make-flags '("PARALLEL=1") ; Allow parallel execution at run-time. + #:make-flags + (list "PARALLEL=1" ; Allow parallel execution at run-time. + (string-append "prefix=" (assoc-ref %outputs "out"))) #:phases (modify-phases %standard-phases (delete 'configure) ; There is no configure phase. - (replace 'install - (lambda _ - (let ((bin (string-append (assoc-ref %outputs "out") "/bin")) - (templates (string-append (assoc-ref %outputs "out") + (add-after 'install 'install-templates + (lambda* (#:key outputs #:allow-other-keys) + (let ((templates (string-append (assoc-ref outputs "out") "/share/delly/templates"))) - (mkdir-p bin) (mkdir-p templates) (copy-recursively "excludeTemplates" templates) - (install-file "src/cov" bin) - (install-file "src/delly" bin) - (install-file "src/dpe" bin))))))) - (native-inputs - `(("python" ,python-2))) + #t)))))) (inputs `(("boost" ,boost) ("htslib" ,htslib) ("zlib" ,zlib) ("bzip2" ,bzip2))) - (home-page "https://github.com/tobiasrausch/delly") + (home-page "https://github.com/dellytools/delly") (synopsis "Integrated structural variant prediction method") (description "Delly is an integrated structural variant prediction method that can discover and genotype deletions, tandem duplications, inversions and @@ -2104,14 +2236,14 @@ accurately delineate genomic rearrangements throughout the genome.") (name "diamond") (version "0.9.22") (source (origin - (method url-fetch) - (uri (string-append - "https://github.com/bbuchfink/diamond/archive/v" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/bbuchfink/diamond.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "0adp87r9ak63frdrdmrdfhsn6g0jnnyq1lr2wibvqbxcl37iir9m")))) + "0bky78v79g3wmdpsd706cscckgw1v09fg8vdd0z8z0d5b97aj9zl")))) (build-system cmake-build-system) (arguments '(#:tests? #f ; no "check" target @@ -2139,13 +2271,14 @@ data and settings.") (version "1.6.0") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/maaskola/discrover/archive/" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/maaskola/discrover.git") + (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 - "0rah9ja4m0rl5mldd6vag9rwrivw1zrqxssfq8qx64m7961fp68k")))) + "173fwi2vb6a5kp406hm3jj6j7v4whww796f2qcygp4rpvamh307y")))) (build-system cmake-build-system) (arguments `(#:tests? #f ; there are no tests @@ -2173,106 +2306,102 @@ of nucleic acid binding proteins.") (license license:gpl3+))) (define-public eigensoft - (let ((revision "1") - (commit "b14d1e202e21e532536ff8004f0419cd5e259dc7")) - (package - (name "eigensoft") - (version (string-append "6.1.2-" - revision "." - (string-take commit 9))) - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/DReichLab/EIG.git") - (commit commit))) - (file-name (string-append "eigensoft-" commit "-checkout")) - (sha256 - (base32 - "0f5m6k2j5c16xc3xbywcs989xyc26ncy1zfzp9j9n55n9r4xcaiq")) - (modules '((guix build utils))) - ;; Remove pre-built binaries. - (snippet '(begin - (delete-file-recursively "bin") - (mkdir "bin") - #t)))) - (build-system gnu-build-system) - (arguments - `(#:tests? #f ; There are no tests. - #:make-flags '("CC=gcc") - #:phases - (modify-phases %standard-phases - ;; There is no configure phase, but the Makefile is in a - ;; sub-directory. - (replace 'configure - (lambda _ - (chdir "src") - ;; The link flags are incomplete. - (substitute* "Makefile" - (("-lgsl") "-lgsl -lm -llapack -llapacke -lpthread")) - #t)) - ;; The provided install target only copies executables to - ;; the "bin" directory in the build root. - (add-after 'install 'actually-install - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (bin (string-append out "/bin"))) - (for-each (lambda (file) - (install-file file bin)) - (find-files "../bin" ".*")) - #t)))))) - (inputs - `(("gsl" ,gsl) - ("lapack" ,lapack) - ("openblas" ,openblas) - ("perl" ,perl) - ("gfortran" ,gfortran "lib"))) - (home-page "https://github.com/DReichLab/EIG") - (synopsis "Tools for population genetics") - (description "The EIGENSOFT package provides tools for population + (package + (name "eigensoft") + (version "7.2.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/DReichLab/EIG.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1c141fqvhnzibmnf22sv23vbmzm20kjjyrib44cfh75wyndp2d9k")) + (modules '((guix build utils))) + ;; Remove pre-built binaries. + (snippet '(begin + (delete-file-recursively "bin") + (mkdir "bin") + #t)))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; There are no tests. + #:make-flags '("CC=gcc") + #:phases + (modify-phases %standard-phases + ;; There is no configure phase, but the Makefile is in a + ;; sub-directory. + (replace 'configure + (lambda _ (chdir "src") #t)) + ;; The provided install target only copies executables to + ;; the "bin" directory in the build root. + (add-after 'install 'actually-install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin"))) + (for-each (lambda (file) + (install-file file bin)) + (find-files "../bin" ".*")) + #t)))))) + (inputs + `(("gsl" ,gsl) + ("lapack" ,lapack) + ("openblas" ,openblas) + ("perl" ,perl) + ("gfortran" ,gfortran "lib"))) + (home-page "https://github.com/DReichLab/EIG") + (synopsis "Tools for population genetics") + (description "The EIGENSOFT package provides tools for population genetics and stratification correction. EIGENSOFT implements methods commonly used in population genetics analyses such as PCA, computation of Tracy-Widom statistics, and finding related individuals in structured populations. It comes with a built-in plotting script and supports multiple file formats and quantitative phenotypes.") - ;; The license of the eigensoft tools is Expat, but since it's - ;; linking with the GNU Scientific Library (GSL) the effective - ;; license is the GPL. - (license license:gpl3+)))) + ;; The license of the eigensoft tools is Expat, but since it's + ;; linking with the GNU Scientific Library (GSL) the effective + ;; license is the GPL. + (license license:gpl3+))) (define-public edirect (package (name "edirect") - (version "4.10") + (version "10.2.20181018") (source (origin (method url-fetch) - (uri (string-append "ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/" - "versions/2016-05-03/edirect.tar.gz")) + (uri (string-append "ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect" + "/versions/" version + "/edirect-" version ".tar.gz")) (sha256 (base32 - "15zsprak5yh8c1yrz4r1knmb5s8qcmdid4xdhkh3lqcv64l60hli")))) + "091f4aigzpbqih6h82nq566gkp3y07i72yqndmqskfgar1vwgci7")))) (build-system perl-build-system) (arguments - `(#:tests? #f ;no "check" target - #:phases + `(#:phases (modify-phases %standard-phases (delete 'configure) (delete 'build) + (delete 'check) ; simple check after install (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let ((target (string-append (assoc-ref outputs "out") - "/bin"))) - (mkdir-p target) - (install-file "edirect.pl" target) - #t))) - (add-after - 'install 'wrap-program - (lambda* (#:key inputs outputs #:allow-other-keys) - ;; Make sure 'edirect.pl' finds all perl inputs at runtime. - (let* ((out (assoc-ref outputs "out")) - (path (getenv "PERL5LIB"))) - (wrap-program (string-append out "/bin/edirect.pl") - `("PERL5LIB" ":" prefix (,path))))))))) + (lambda* (#:key outputs #:allow-other-keys) + (install-file "edirect.pl" + (string-append (assoc-ref outputs "out") "/bin")) + #t)) + (add-after 'install 'wrap-program + (lambda* (#:key outputs #:allow-other-keys) + ;; Make sure 'edirect.pl' finds all perl inputs at runtime. + (let* ((out (assoc-ref outputs "out")) + (path (getenv "PERL5LIB"))) + (wrap-program (string-append out "/bin/edirect.pl") + `("PERL5LIB" ":" prefix (,path)))) + #t)) + (add-after 'wrap-program 'check + (lambda* (#:key outputs #:allow-other-keys) + (invoke (string-append (assoc-ref outputs "out") + "/bin/edirect.pl") + "-filter" "-help") + #t))))) (inputs `(("perl-html-parser" ,perl-html-parser) ("perl-encode-locale" ,perl-encode-locale) @@ -2288,6 +2417,7 @@ quantitative phenotypes.") ("perl-net-http" ,perl-net-http) ("perl-uri" ,perl-uri) ("perl-www-robotrules" ,perl-www-robotrules) + ("perl-xml-simple" ,perl-xml-simple) ("perl" ,perl))) (home-page "http://www.ncbi.nlm.nih.gov/books/NBK179288/") (synopsis "Tools for accessing the NCBI's set of databases") @@ -2383,17 +2513,16 @@ ChIP-Seq, and analysis of metagenomic data.") (define-public express-beta-diversity (package (name "express-beta-diversity") - (version "1.0.7") + (version "1.0.8") (source (origin - (method url-fetch) - (uri - (string-append - "https://github.com/dparks1134/ExpressBetaDiversity/archive/v" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/dparks1134/ExpressBetaDiversity.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "1djvdlmqvjf6h0zq7w36y8cl5cli6rgj86x65znl48agnwmzxfxr")))) + "0s0yzg5c21349rh7x4w9266jsvnp7j1hp9cf8sk32hz8nvrj745x")))) (build-system gnu-build-system) (arguments `(#:phases @@ -2401,17 +2530,13 @@ ChIP-Seq, and analysis of metagenomic data.") (delete 'configure) (add-before 'build 'enter-source (lambda _ (chdir "source") #t)) (replace 'check - (lambda _ (zero? (system* "../bin/ExpressBetaDiversity" - "-u")))) - (add-after 'check 'exit-source (lambda _ (chdir "..") #t)) + (lambda _ (invoke "../bin/ExpressBetaDiversity" "-u") #t)) (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let ((bin (string-append (assoc-ref outputs "out") - "/bin"))) - (mkdir-p bin) - (install-file "scripts/convertToEBD.py" bin) - (install-file "bin/ExpressBetaDiversity" bin) - #t)))))) + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) + (install-file "../scripts/convertToEBD.py" bin) + (install-file "../bin/ExpressBetaDiversity" bin) + #t)))))) (inputs `(("python" ,python-2))) (home-page "http://kiwi.cs.dal.ca/Software/ExpressBetaDiversity") @@ -2444,31 +2569,30 @@ similarity of community members.") (delete 'configure) (replace 'build (lambda* (#:key source #:allow-other-keys) - (and (zero? (system* "gcc" - "-O3" - "-finline-functions" - "-funroll-loops" - "-Wall" - "-o" - "FastTree" - source - "-lm")) - (zero? (system* "gcc" - "-DOPENMP" - "-fopenmp" - "-O3" - "-finline-functions" - "-funroll-loops" - "-Wall" - "-o" - "FastTreeMP" - source - "-lm"))))) + (invoke "gcc" + "-O3" + "-finline-functions" + "-funroll-loops" + "-Wall" + "-o" + "FastTree" + source + "-lm") + (invoke "gcc" + "-DOPENMP" + "-fopenmp" + "-O3" + "-finline-functions" + "-funroll-loops" + "-Wall" + "-o" + "FastTreeMP" + source + "-lm") + #t)) (replace 'install (lambda* (#:key outputs #:allow-other-keys) - (let ((bin (string-append (assoc-ref outputs "out") - "/bin"))) - (mkdir-p bin) + (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) (install-file "FastTree" bin) (install-file "FastTreeMP" bin) #t)))))) @@ -2515,38 +2639,39 @@ results. The FASTX-Toolkit tools perform some of these preprocessing tasks.") (define-public flexbar (package (name "flexbar") - (version "2.5") + (version "3.4.0") (source (origin - (method url-fetch) - (uri - (string-append "mirror://sourceforge/flexbar/" - version "/flexbar_v" version "_src.tgz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/seqan/flexbar.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "13jaykc3y1x8y5nn9j8ljnb79s5y51kyxz46hdmvvjj6qhyympmf")))) + "1pq9sxvdnldl14libk234m72dqhwgzs3acgl943wchwdqlcsi5r2")))) (build-system cmake-build-system) (arguments - `(#:configure-flags (list - (string-append "-DFLEXBAR_BINARY_DIR=" - (assoc-ref %outputs "out") - "/bin/")) - #:phases + `(#:phases (modify-phases %standard-phases (replace 'check (lambda* (#:key outputs #:allow-other-keys) - (setenv "PATH" (string-append - (assoc-ref outputs "out") "/bin:" - (getenv "PATH"))) - (chdir "../flexbar_v2.5_src/test") - (zero? (system* "bash" "flexbar_validate.sh")))) - (delete 'install)))) + (setenv "PATH" (string-append (getcwd) ":" (getenv "PATH"))) + (with-directory-excursion "../source/test" + (invoke "bash" "flexbar_test.sh")) + #t)) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (string-append (assoc-ref outputs "out"))) + (bin (string-append out "/bin/"))) + (install-file "flexbar" bin)) + #t))))) (inputs `(("tbb" ,tbb) ("zlib" ,zlib))) (native-inputs `(("pkg-config" ,pkg-config) ("seqan" ,seqan))) - (home-page "http://flexbar.sourceforge.net") + (home-page "https://github.com/seqan/flexbar") (synopsis "Barcode and adapter removal tool for sequencing platforms") (description "Flexbar preprocesses high-throughput nucleotide sequencing data @@ -2555,7 +2680,7 @@ Moreover, trimming and filtering features are provided. Flexbar increases read mapping rates and improves genome and transcriptome assemblies. It supports next-generation sequencing data in fasta/q and csfasta/q format from Illumina, Roche 454, and the SOLiD platform.") - (license license:gpl3))) + (license license:bsd-3))) (define-public fraggenescan (package @@ -2596,8 +2721,10 @@ Illumina, Roche 454, and the SOLiD platform.") (string-append " strcpy(train_dir, \"" share "/train/\");")))) #t)) (replace 'build - (lambda _ (and (zero? (system* "make" "clean")) - (zero? (system* "make" "fgs"))))) + (lambda _ + (invoke "make" "clean") + (invoke "make" "fgs") + #t)) (replace 'install (lambda* (#:key outputs #:allow-other-keys) (let* ((out (string-append (assoc-ref outputs "out"))) @@ -2605,7 +2732,8 @@ Illumina, Roche 454, and the SOLiD platform.") (share (string-append out "/share/fraggenescan/train"))) (install-file "run_FragGeneScan.pl" bin) (install-file "FragGeneScan" bin) - (copy-recursively "train" share)))) + (copy-recursively "train" share)) + #t)) (delete 'check) (add-after 'install 'post-install-check ;; In lieu of 'make check', run one of the examples and check the @@ -2614,21 +2742,24 @@ Illumina, Roche 454, and the SOLiD platform.") (let* ((out (string-append (assoc-ref outputs "out"))) (bin (string-append out "/bin/")) (frag (string-append bin "run_FragGeneScan.pl"))) - (and (zero? (system* frag ; Test complete genome. - "-genome=./example/NC_000913.fna" - "-out=./test2" - "-complete=1" - "-train=complete")) - (file-exists? "test2.faa") - (file-exists? "test2.ffn") - (file-exists? "test2.gff") - (file-exists? "test2.out") - (zero? (system* ; Test incomplete sequences. - frag - "-genome=./example/NC_000913-fgs.ffn" - "-out=out" - "-complete=0" - "-train=454_30"))))))))) + ;; Test complete genome. + (invoke frag + "-genome=./example/NC_000913.fna" + "-out=./test2" + "-complete=1" + "-train=complete") + (unless (and (file-exists? "test2.faa") + (file-exists? "test2.ffn") + (file-exists? "test2.gff") + (file-exists? "test2.out")) + (error "Expected files do not exist.")) + ;; Test incomplete sequences. + (invoke frag + "-genome=./example/NC_000913-fgs.ffn" + "-out=out" + "-complete=0" + "-train=454_30") + #t)))))) (inputs `(("perl" ,perl) ("python" ,python-2))) ;not compatible with python 3. @@ -2648,16 +2779,14 @@ genes in incomplete assemblies or complete genomes.") (version "2.3") (source (origin - (method url-fetch) - (uri (string-append - "https://github.com/ctSkennerton/fxtract/archive/" - version ".tar.gz")) - (file-name (string-append "ctstennerton-util-" - (string-take util-commit 7) - "-checkout")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/ctSkennerton/fxtract.git") + (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 - "0275cfdhis8517hm01is62062swmi06fxzifq7mr3knbbxjlaiwj")))) + "0hab3gpwf4w9s87qlbswq6ws1qqybh4dcqk79q1ahyldzai5fgp5")))) (build-system gnu-build-system) (arguments `(#:make-flags (list @@ -2711,19 +2840,22 @@ comment or quality sections.") (define-public gemma (package (name "gemma") - (version "0.96") + (version "0.98") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/xiangzhou/GEMMA/archive/v" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/xiangzhou/GEMMA.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "055ynn16gd12pf78n4vr2a9jlwsbwzajpdnf2y2yilg1krfff222")) - (patches (search-patches "gemma-intel-compat.patch")))) + "1s3ncnbn45r2hh1cvrqky1kbqq6546biypr4f5mkw1kqlrgyh0yg")))) (inputs - `(("gsl" ,gsl) + `(("eigen" ,eigen) + ("gfortran" ,gfortran "lib") + ("gsl" ,gsl) ("lapack" ,lapack) + ("openblas" ,openblas) ("zlib" ,zlib))) (build-system gnu-build-system) (arguments @@ -2738,6 +2870,15 @@ comment or quality sections.") #:phases (modify-phases %standard-phases (delete 'configure) + (add-after 'unpack 'find-eigen + (lambda* (#:key inputs #:allow-other-keys) + ;; Ensure that Eigen headers can be found + (setenv "CPLUS_INCLUDE_PATH" + (string-append (getenv "CPLUS_INCLUDE_PATH") + ":" + (assoc-ref inputs "eigen") + "/include/eigen3")) + #t)) (add-before 'build 'bin-mkdir (lambda _ (mkdir-p "bin") @@ -2761,16 +2902,16 @@ association studies (GWAS).") (define-public grit (package (name "grit") - (version "2.0.2") + (version "2.0.5") (source (origin - (method url-fetch) - (uri (string-append - "https://github.com/nboley/grit/archive/" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/nboley/grit.git") + (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 - "157in84dj70wimbind3x7sy1whs3h57qfgcnj2s6lrd38fbrb7mj")))) + "1l5v8vfvfbrpmgnrvbrbv40d0arhxcnmxgv2f1mlcqfa3q6bkqm9")))) (build-system python-build-system) (arguments `(#:python ,python-2 @@ -2782,13 +2923,7 @@ association studies (GWAS).") (delete-file "grit/sparsify_support_fns.c") (delete-file "grit/call_peaks_support_fns.c") (substitute* "setup.py" - (("Cython.Setup") "Cython.Build") - ;; Add numpy include path to fix compilation - (("pyx\", \\]") - (string-append "pyx\", ], include_dirs = ['" - (assoc-ref inputs "python-numpy") - "/lib/python2.7/site-packages/numpy/core/include/" - "']"))) + (("Cython.Setup") "Cython.Build")) #t))))) (inputs `(("python-scipy" ,python2-scipy) @@ -2882,16 +3017,11 @@ particular, reads spanning multiple exons.") (source (origin (method url-fetch) - ;; FIXME: a better source URL is - ;; (string-append "ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2" - ;; "/downloads/hisat2-" version "-source.zip") - ;; with hash "0lywnr8kijwsc2aw10dwxic0n0yvip6fl3rjlvc8zzwahamy4x7g" - ;; but it is currently unavailable. - (uri "https://github.com/infphilo/hisat2/archive/cba6e8cb.tar.gz") - (file-name (string-append name "-" version ".tar.gz")) + (uri (string-append "ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2" + "/downloads/hisat2-" version "-source.zip")) (sha256 (base32 - "1mf2hdsyv7cd97xm9mp9a4qws02yrj95y6w6f6cdwnq0klp81r50")))) + "0lywnr8kijwsc2aw10dwxic0n0yvip6fl3rjlvc8zzwahamy4x7g")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; no check target @@ -2941,18 +3071,15 @@ indexing scheme is called a @dfn{Hierarchical Graph FM index} (HGFM).") (define-public hmmer (package (name "hmmer") - (version "3.1b2") + (version "3.2.1") (source (origin (method url-fetch) (uri (string-append - "http://eddylab.org/software/hmmer" - (version-major version) "/" - version "/hmmer-" version ".tar.gz")) + "http://eddylab.org/software/hmmer/hmmer-" version ".tar.gz")) (sha256 (base32 - "0djmgc0pfli0jilfx8hql1axhwhqxqb8rxg2r5rg07aw73sfs5nx")) - (patches (search-patches "hmmer-remove-cpu-specificity.patch")))) + "171bivy6xhgjsz5nv53n81pc3frnwz29ylblawk2bv46szwjjqd5")))) (build-system gnu-build-system) (native-inputs `(("perl" ,perl))) (home-page "http://hmmer.org/") @@ -2962,12 +3089,10 @@ indexing scheme is called a @dfn{Hierarchical Graph FM index} (HGFM).") sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs).") - (license (list license:gpl3+ - ;; The bundled library 'easel' is distributed - ;; under The Janelia Farm Software License. - (license:non-copyleft - "file://easel/LICENSE" - "See easel/LICENSE in the distribution."))))) + ;; hmmer uses non-portable SSE intrinsics so building fails on other + ;; platforms. + (supported-systems '("x86_64-linux" "i686-linux")) + (license license:bsd-3))) (define-public htseq (package @@ -3003,14 +3128,14 @@ from high-throughput sequencing assays.") (name "java-htsjdk") (version "2.3.0") ; last version without build dependency on gradle (source (origin - (method url-fetch) - (uri (string-append - "https://github.com/samtools/htsjdk/archive/" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/samtools/htsjdk.git") + (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 - "1ibhzzxsfc38nqyk9r8zqj6blfc1kh26iirypd4q6n90hs2m6nyq")) + "1b178ixcabanm834ydjl3jiakpyxdmki32hqfv2abrzn3rcwa28i")) (modules '((guix build utils))) (snippet ;; Delete pre-built binaries @@ -3357,26 +3482,28 @@ VCF.") (lambda* (#:key inputs #:allow-other-keys) (mkdir-p "lib/jni") (mkdir-p "jdk-src") - (and (zero? (system* "tar" "--strip-components=1" "-C" "jdk-src" - "-xf" (assoc-ref inputs "jdk-src"))) - (zero? (system* "javah" "-jni" - "-classpath" "classes" - "-d" "lib/" - "net.sf.samtools.util.zip.IntelDeflater")) - (with-directory-excursion "src/c/inteldeflater" - (zero? (system* "gcc" "-I../../../lib" "-I." - (string-append "-I" (assoc-ref inputs "jdk") - "/include/linux") - "-I../../../jdk-src/src/share/native/common/" - "-I../../../jdk-src/src/solaris/native/common/" - "-c" "-O3" "-fPIC" "IntelDeflater.c")) - (zero? (system* "gcc" "-shared" - "-o" "../../../lib/jni/libIntelDeflater.so" - "IntelDeflater.o" "-lz" "-lstdc++")))))) + (invoke "tar" "--strip-components=1" "-C" "jdk-src" + "-xf" (assoc-ref inputs "jdk-src")) + (invoke "javah" "-jni" + "-classpath" "classes" + "-d" "lib/" + "net.sf.samtools.util.zip.IntelDeflater") + (with-directory-excursion "src/c/inteldeflater" + (invoke "gcc" "-I../../../lib" "-I." + (string-append "-I" (assoc-ref inputs "jdk") + "/include/linux") + "-I../../../jdk-src/src/share/native/common/" + "-I../../../jdk-src/src/solaris/native/common/" + "-c" "-O3" "-fPIC" "IntelDeflater.c") + (invoke "gcc" "-shared" + "-o" "../../../lib/jni/libIntelDeflater.so" + "IntelDeflater.o" "-lz" "-lstdc++")) + #t)) ;; We can only build everything else after building the JNI library. (add-after 'build-jni 'build-rest (lambda* (#:key make-flags #:allow-other-keys) - (zero? (apply system* `("ant" "all" ,@make-flags))))) + (apply invoke `("ant" "all" ,@make-flags)) + #t)) (add-before 'build 'set-JAVA6_HOME (lambda _ (setenv "JAVA6_HOME" (getenv "JAVA_HOME")) @@ -3522,7 +3649,7 @@ performance.") (define-public htslib (package (name "htslib") - (version "1.8") + (version "1.9") (source (origin (method url-fetch) (uri (string-append @@ -3530,7 +3657,7 @@ performance.") version "/htslib-" version ".tar.bz2")) (sha256 (base32 - "18bw0mn9pj5wgarnlaxmf1bb8pdqgl1zd6czirqcr62ajpn1xvy0")))) + "16ljv43sc3fxmv63w7b2ff8m1s7h89xhazwmbm1bicz8axq8fjz0")))) (build-system gnu-build-system) (inputs `(("openssl" ,openssl) @@ -3567,14 +3694,14 @@ data. It also provides the @command{bgzip}, @command{htsfile}, and (name "idr") (version "2.0.3") (source (origin - (method url-fetch) - (uri (string-append - "https://github.com/nboley/idr/archive/" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/nboley/idr.git") + (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 - "1rjdly6daslw66r43g9md8znizlscn1sphycqyldzsidkc4vxqv3")) + "04j876h6z444v2q79drxx283d3k5snd72kj895wbalnl42206x9g")) ;; Delete generated C code. (snippet '(begin (delete-file "idr/inv_cdf.c") #t)))) @@ -3601,7 +3728,7 @@ experiments and provide highly stable thresholds based on reproducibility.") (define-public jellyfish (package (name "jellyfish") - (version "2.2.7") + (version "2.2.10") (source (origin (method url-fetch) (uri (string-append "https://github.com/gmarcais/Jellyfish/" @@ -3609,7 +3736,7 @@ experiments and provide highly stable thresholds based on reproducibility.") "/jellyfish-" version ".tar.gz")) (sha256 (base32 - "1a1iwq9pq54k2m9ypvwl5s0bqfl64gwh9dx5af9i382ajas2016q")))) + "1k4pc3fvv6w1km2yph4m5sd78fbxp21d6xyzgmy0gjihzc6mb249")))) (build-system gnu-build-system) (outputs '("out" ;for library "ruby" ;for Ruby bindings @@ -3646,8 +3773,8 @@ DNA sequences. It outputs its k-mer counts in a binary format, which can be translated into a human-readable text format using the @code{jellyfish dump} command, or queried for specific k-mers with @code{jellyfish query}.") (home-page "http://www.genome.umd.edu/jellyfish.html") - ;; From their website: JELLYFISH runs on 64-bit Intel-compatible processors - (supported-systems '("x86_64-linux")) + ;; JELLYFISH seems to be 64-bit only. + (supported-systems '("x86_64-linux" "aarch64-linux" "mips64el-linux")) ;; The combined work is published under the GPLv3 or later. Individual ;; files such as lib/jsoncpp.cpp are released under the Expat license. (license (list license:gpl3+ license:expat)))) @@ -3655,75 +3782,48 @@ command, or queried for specific k-mers with @code{jellyfish query}.") (define-public khmer (package (name "khmer") - (version "2.0") + (version "2.1.2") (source (origin - (method url-fetch) - (uri (pypi-uri "khmer" version)) + (method git-fetch) + (uri (git-reference + (url "https://github.com/dib-lab/khmer.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "0wb05shqh77v00256qlm68vbbx3kl76fyzihszbz5nhanl4ni33a")) - (patches (search-patches "khmer-use-libraries.patch")))) + "02x38d9jw2r58y8dmnj4hffy9wxv1yc1jwbvdbhby9dxndv94r9m")) + (patches (search-patches "khmer-use-libraries.patch")) + (modules '((guix build utils))) + (snippet + '(begin + ;; Delete bundled libraries. We do not replace the bundled seqan + ;; as it is a modified subset of the old version 1.4.1. + ;; + ;; We do not replace the bundled MurmurHash as the canonical + ;; repository for this code 'SMHasher' is unsuitable for providing + ;; a library. See + ;; https://lists.gnu.org/archive/html/guix-devel/2016-06/msg00977.html + (delete-file-recursively "third-party/zlib") + (delete-file-recursively "third-party/bzip2") + #t)))) (build-system python-build-system) (arguments `(#:phases (modify-phases %standard-phases - (add-after 'unpack 'set-paths - (lambda* (#:key inputs outputs #:allow-other-keys) - ;; Delete bundled libraries. - (delete-file-recursively "third-party/zlib") - (delete-file-recursively "third-party/bzip2") - ;; Replace bundled seqan. - (let* ((seqan-all "third-party/seqan") - (seqan-include (string-append - seqan-all "/core/include"))) - (delete-file-recursively seqan-all) - (copy-recursively (string-append (assoc-ref inputs "seqan") - "/include/seqan") - (string-append seqan-include "/seqan"))) - ;; We do not replace the bundled MurmurHash as the canonical - ;; repository for this code 'SMHasher' is unsuitable for - ;; providing a library. See - ;; https://lists.gnu.org/archive/html/guix-devel/2016-06/msg00977.html - #t)) (add-after 'unpack 'set-cc - (lambda _ - (setenv "CC" "gcc") - #t)) - ;; It is simpler to test after installation. - (delete 'check) - (add-after 'install 'post-install-check - (lambda* (#:key inputs outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out"))) - (setenv "PATH" - (string-append - (getenv "PATH") - ":" - (assoc-ref outputs "out") - "/bin")) - (setenv "PYTHONPATH" - (string-append - (getenv "PYTHONPATH") - ":" - out - "/lib/python" - (string-take (string-take-right - (assoc-ref inputs "python") 5) 3) - "/site-packages")) - (with-directory-excursion "build" - (zero? (system* "nosetests" "khmer" "--attr" - "!known_failing"))))))))) + (lambda _ (setenv "CC" "gcc") #t)) + ;; FIXME: This fails with "permission denied". + (delete 'reset-gzip-timestamps)))) (native-inputs - `(("seqan" ,seqan) - ("python-nose" ,python-nose))) + `(("python-cython" ,python-cython) + ("python-pytest" ,python-pytest) + ("python-pytest-runner" ,python-pytest-runner))) (inputs `(("zlib" ,zlib) ("bzip2" ,bzip2) ("python-screed" ,python-screed) - ("python-bz2file" ,python-bz2file) - ;; Tests fail when gcc-5 is used for compilation. Use gcc-4.9 at least - ;; until the next version of khmer (likely 2.1) is released. - ("gcc" ,gcc-4.9))) + ("python-bz2file" ,python-bz2file))) (home-page "https://khmer.readthedocs.org/") (synopsis "K-mer counting, filtering and graph traversal library") (description "The khmer software is a set of command-line tools for @@ -3739,16 +3839,16 @@ data.") (define-public kaiju (package (name "kaiju") - (version "1.6.2") + (version "1.6.3") (source (origin - (method url-fetch) - (uri (string-append - "https://github.com/bioinformatics-centre/kaiju/archive/v" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/bioinformatics-centre/kaiju") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "1kdn4rxs0kr9ibmrgrfcci71aa6j6gr71dbc8pff7731rpab6kj7")))) + "119pzi0ddzv9mjg4wwa6han0cwr3k3ssn7kirvsjfcq05mi5ka0x")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; There are no tests. @@ -3762,8 +3862,7 @@ data.") (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) (mkdir-p bin) (chdir "..") - (copy-recursively "bin" bin) - (copy-recursively "util" bin)) + (copy-recursively "bin" bin)) #t))))) (inputs `(("perl" ,perl) @@ -3891,16 +3990,16 @@ sequences).") (define-public mash (package (name "mash") - (version "2.0") + (version "2.1") (source (origin - (method url-fetch) - (uri (string-append - "https://github.com/marbl/mash/archive/v" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/marbl/mash.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "00fx14vpmgsijwxd1xql3if934l82v8ckqgjjyyhnr36qb9qrskv")) + "049hwcc059p2fd9vwndn63laifvvsi0wmv84i6y1fr79k15dxwy6")) (modules '((guix build utils))) (snippet '(begin @@ -3925,9 +4024,7 @@ sequences).") "src/mash/CommandScreen.cpp") (("^#include \"kseq\\.h\"") "#include \"htslib/kseq.h\"")) - #t)) - (add-after 'fix-includes 'autoconf - (lambda _ (zero? (system* "autoconf"))))))) + #t))))) (native-inputs `(("autoconf" ,autoconf) ;; Capnproto and htslib are statically embedded in the final @@ -3954,13 +4051,14 @@ form of assemblies or reads.") (version "2.12.1") (source (origin - (method url-fetch) - (uri (string-append "https://bitbucket.org/berkeleylab/metabat/get/v" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://bitbucket.org/berkeleylab/metabat.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "1hmvdalz3zj5sqqklg0l4npjdv37cv2hsdi1al9iby2ndxjs1b73")) + "0hyg2smw1nz69mfvjpk45xyyychmda92c80a0cv7baji84ri4iyn")) (patches (search-patches "metabat-fix-compilation.patch")))) (build-system scons-build-system) (arguments @@ -4023,16 +4121,16 @@ probabilistic distances of genome abundance and tetranucleotide frequency.") (define-public minced (package (name "minced") - (version "0.2.0") + (version "0.3.2") (source (origin - (method url-fetch) - (uri (string-append - "https://github.com/ctSkennerton/minced/archive/" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/ctSkennerton/minced.git") + (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 - "0wxmlsapxfpxfd3ps9636h7i2xy6la8i42mwh0j2lsky63h63jp1")))) + "1f5h9him0gd355cnx7p6pnxpknhckd4g0v62mg8zyhfbx9as25fv")))) (build-system gnu-build-system) (arguments `(#:test-target "test" @@ -4061,7 +4159,8 @@ probabilistic distances of genome abundance and tetranucleotide frequency.") "#!" (assoc-ref inputs "bash") "/bin/sh\n\n" (assoc-ref inputs "jre") "/bin/java -jar " bin "/minced.jar \"$@\"\n")))) - (chmod wrapper #o555))))))) + (chmod wrapper #o555)) + #t))))) (native-inputs `(("jdk" ,icedtea "jdk"))) (inputs @@ -4144,12 +4243,13 @@ that a read originated from a particular isoform.") (delete 'configure) (replace 'check ;; There are no tests, so just test if it runs. - (lambda _ (zero? (system* "./muscle" "-version")))) + (lambda _ (invoke "./muscle" "-version") #t)) (replace 'install (lambda* (#:key outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) (bin (string-append out "/bin"))) - (install-file "muscle" bin))))))) + (install-file "muscle" bin) + #t)))))) (home-page "http://www.drive5.com/muscle") (synopsis "Multiple sequence alignment program") (description @@ -4174,11 +4274,6 @@ program for nucleotide and protein sequences.") (base32 "1hkw21rq1mwf7xp0rmbb2gqc0i6p11108m69i7mr7xcjl268pxnb")))) (build-system gnu-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'autoconf - (lambda _ (zero? (system* "autoreconf" "-vif"))))))) (inputs ;; XXX: TODO: Enable Lua and Guile bindings. ;; https://github.com/tjunier/newick_utils/issues/13 @@ -4223,19 +4318,20 @@ interrupted by stop codons. OrfM finds and prints these ORFs.") (license license:lgpl3+))) (define-public pplacer - (let ((commit "g807f6f3")) + (let ((commit "807f6f3")) (package (name "pplacer") ;; The commit should be updated with each version change. (version "1.1.alpha19") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/matsen/pplacer/archive/v" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/matsen/pplacer.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 - (base32 "0z1lnd2s8sh6kpzg106wzbh2szw7h0hvq8syd5a6wv4rmyyz6x0f")))) + (base32 "11ppbbbx20p2g9wj3ff64dhnarb12q79v7qh4rk0gj6lkbz4n7cn")))) (build-system ocaml-build-system) (arguments `(#:ocaml ,ocaml-4.01 @@ -4252,11 +4348,12 @@ interrupted by stop codons. OrfM finds and prints these ORFs.") (local-dir "cddlib_guix")) (mkdir local-dir) (with-directory-excursion local-dir - (system* "tar" "xvf" cddlib-src)) + (invoke "tar" "xvf" cddlib-src)) (let ((cddlib-src-folder (string-append local-dir "/" (list-ref (scandir local-dir) 2) "/lib-src"))) + (for-each make-file-writable (find-files "cdd_src" ".*")) (for-each (lambda (file) (copy-file file @@ -4318,10 +4415,9 @@ downstream analysis.") #:phases (modify-phases %standard-phases (add-after 'unpack 'enter-scripts-dir - (lambda _ (chdir "scripts"))) + (lambda _ (chdir "scripts") #t)) (replace 'check - (lambda _ - (zero? (system* "python" "-m" "unittest" "discover" "-v")))) + (lambda _ (invoke "python" "-m" "unittest" "discover" "-v") #t)) (add-after 'install 'wrap-executables (lambda* (#:key inputs outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) @@ -4581,13 +4677,14 @@ large-scale data and can be applied to hundreds of species at once.") (version "2.0.7") (source (origin - (method url-fetch) - (uri (string-append "https://bitbucket.org/regulatorygenomicsupf/" - "pyicoteo/get/v" version ".tar.bz2")) - (file-name (string-append name "-" version ".tar.bz2")) + (method git-fetch) + (uri (git-reference + (url "https://bitbucket.org/regulatorygenomicsupf/pyicoteo.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "0d6087f29xp8wxwlj111c3sylli98n0l8ry58c51ixzq0zfm50wa")))) + "0hz5g8d25lbjy1wpscr490l0lmyvaix893hhax4fxnh1h9w34w8p")))) (build-system python-build-system) (arguments `(#:python ,python-2 ; does not work with Python 3 @@ -4618,14 +4715,14 @@ different command-line tools: (name "prodigal") (version "2.6.3") (source (origin - (method url-fetch) - (uri (string-append - "https://github.com/hyattpd/Prodigal/archive/v" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/hyattpd/Prodigal.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "17srxkqd3jc77xk15pfbgg1a9xahqg7337w95mrsia7mpza4l2c9")))) + "1fs1hqk83qjbjhrvhw6ni75zakx5ki1ayy3v6wwkn3xvahc9hi5s")))) (build-system gnu-build-system) (arguments `(#:tests? #f ;no check target @@ -4671,10 +4768,11 @@ partial genes, and identifies translation initiation sites.") (getenv "PATH"))) (setenv "PERL5LIB" (string-append (getcwd) "/lib" ":" (getenv "PERL5LIB"))) - (zero? (length (filter (lambda (file) - (display file)(display "\n") - (not (zero? (system* "perl" file)))) - (find-files "t" ".*\\.t$")))))) + (for-each (lambda (file) + (display file)(display "\n") + (invoke "perl" file)) + (find-files "t" ".*\\.t$")) + #t)) (replace 'install ;; There is no 'install' target in the Makefile. (lambda* (#:key outputs #:allow-other-keys) @@ -4763,18 +4861,17 @@ extremely diverse sets of genomes.") (define-public raxml (package (name "raxml") - (version "8.2.10") + (version "8.2.12") (source (origin - (method url-fetch) - (uri - (string-append - "https://github.com/stamatak/standard-RAxML/archive/v" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/stamatak/standard-RAxML.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "13s7aspfdcfr6asynwdg1x6vznys6pzap5f8wsffbnnwpkkg9ya8")))) + "1jqjzhch0rips0vp04prvb8vmc20c5pdmsqn8knadcf91yy859fh")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; There are no tests. @@ -4805,66 +4902,79 @@ phylogenies.") (define-public rsem (package (name "rsem") - (version "1.2.20") + (version "1.3.1") (source (origin - (method url-fetch) - (uri - (string-append "http://deweylab.biostat.wisc.edu/rsem/src/rsem-" - version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/deweylab/RSEM.git") + (commit (string-append "v" version)))) (sha256 - (base32 "0nzdc0j0hjllhsd5f2xli95dafm3nawskigs140xzvjk67xh0r9q")) - (patches (search-patches "rsem-makefile.patch")) + (base32 "1jlq11d1p8qp64w75yj8cnbbd1a93viq10pzsbwal7vdn8fg13j1")) + (file-name (git-file-name name version)) (modules '((guix build utils))) (snippet '(begin - ;; remove bundled copy of boost + ;; remove bundled copy of boost and samtools (delete-file-recursively "boost") + (delete-file-recursively "samtools-1.3") #t)))) (build-system gnu-build-system) (arguments `(#:tests? #f ;no "check" target + #:make-flags + (list (string-append "BOOST=" + (assoc-ref %build-inputs "boost") + "/include/") + (string-append "SAMHEADERS=" + (assoc-ref %build-inputs "htslib") + "/include/htslib/sam.h") + (string-append "SAMLIBS=" + (assoc-ref %build-inputs "htslib") + "/lib/libhts.a")) #:phases (modify-phases %standard-phases ;; No "configure" script. ;; Do not build bundled samtools library. (replace 'configure - (lambda _ - (substitute* "Makefile" - (("^all : sam/libbam.a") "all : ")) - #t)) + (lambda _ + (substitute* "Makefile" + (("^all : \\$\\(PROGRAMS\\).*") "all: $(PROGRAMS)\n") + (("^\\$\\(SAMLIBS\\).*") "")) + #t)) (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (string-append (assoc-ref outputs "out"))) - (bin (string-append out "/bin/")) - (perl (string-append out "/lib/perl5/site_perl"))) - (mkdir-p bin) - (mkdir-p perl) - (for-each (lambda (file) - (install-file file bin)) - (find-files "." "rsem-.*")) - (install-file "rsem_perl_utils.pm" perl)) - #t)) - (add-after - 'install 'wrap-program - (lambda* (#:key outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out"))) - (for-each (lambda (prog) - (wrap-program (string-append out "/bin/" prog) - `("PERL5LIB" ":" prefix - (,(string-append out "/lib/perl5/site_perl"))))) - '("rsem-plot-transcript-wiggles" - "rsem-calculate-expression" - "rsem-generate-ngvector" - "rsem-run-ebseq" - "rsem-prepare-reference"))) - #t))))) + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (string-append (assoc-ref outputs "out"))) + (bin (string-append out "/bin/")) + (perl (string-append out "/lib/perl5/site_perl"))) + (mkdir-p bin) + (mkdir-p perl) + (for-each (lambda (file) + (install-file file bin)) + (find-files "." "rsem-.*")) + (install-file "rsem_perl_utils.pm" perl)) + #t)) + (add-after 'install 'wrap-program + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (for-each (lambda (prog) + (wrap-program (string-append out "/bin/" prog) + `("PERL5LIB" ":" prefix + (,(string-append out "/lib/perl5/site_perl"))))) + '("rsem-calculate-expression" + "rsem-control-fdr" + "rsem-generate-data-matrix" + "rsem-generate-ngvector" + "rsem-plot-transcript-wiggles" + "rsem-prepare-reference" + "rsem-run-ebseq" + "rsem-run-prsem-testing-procedure"))) + #t))))) (inputs `(("boost" ,boost) - ("ncurses" ,ncurses) ("r-minimal" ,r-minimal) ("perl" ,perl) - ("samtools" ,samtools-0.1) + ("htslib" ,htslib-1.3) ("zlib" ,zlib))) (home-page "http://deweylab.biostat.wisc.edu/rsem/") (synopsis "Estimate gene expression levels from RNA-Seq data") @@ -4954,21 +5064,24 @@ distribution, coverage uniformity, strand specificity, etc.") (modify-phases %standard-phases (replace 'bootstrap (lambda _ - (invoke "bash" "gen_auto"))) + (substitute* "gen_tools_am" + (("/usr/bin/env.*") (which "perl"))) + (invoke "bash" "gen_auto") + #t)) (add-after 'build 'build-additional-tools (lambda* (#:key make-flags #:allow-other-keys) - (every (lambda (dir) - (with-directory-excursion (string-append "tools/" dir) - (zero? (apply system* "make" make-flags)))) - dirs))) + (for-each (lambda (dir) + (with-directory-excursion (string-append "tools/" dir) + (apply invoke "make" make-flags))) + dirs) + #t)) (add-after 'install 'install-additional-tools (lambda* (#:key make-flags #:allow-other-keys) - (fold (lambda (dir result) - (with-directory-excursion (string-append "tools/" dir) - (and result - (zero? (apply system* - `("make" ,@make-flags "install")))))) - #t dirs))))))) + (for-each (lambda (dir) + (with-directory-excursion (string-append "tools/" dir) + (apply invoke `("make" ,@make-flags "install")))) + dirs) + #t)))))) (inputs `(("gsl" ,gsl) ("boost" ,boost) @@ -4994,7 +5107,7 @@ to the user's query of interest.") (define-public samtools (package (name "samtools") - (version "1.8") + (version "1.9") (source (origin (method url-fetch) @@ -5003,15 +5116,19 @@ to the user's query of interest.") version "/samtools-" version ".tar.bz2")) (sha256 (base32 - "05myg7bs90i68qbqab9cdg9rqj2xh39azibrx82ipzc5kcfvqhn9")))) + "10ilqbmm7ri8z431sn90lvbjwizd0hhkf9rcqw8j823hf26nhgq8")) + (modules '((guix build utils))) + (snippet '(begin + ;; Delete bundled htslib. + (delete-file-recursively "htslib-1.9") + #t)))) (build-system gnu-build-system) (arguments `(#:modules ((ice-9 ftw) (ice-9 regex) (guix build gnu-build-system) (guix build utils)) - #:make-flags (list (string-append "prefix=" (assoc-ref %outputs "out"))) - #:configure-flags (list "--with-ncurses" "--with-htslib=system") + #:configure-flags (list "--with-ncurses") #:phases (modify-phases %standard-phases (add-after 'unpack 'patch-tests @@ -5065,9 +5182,9 @@ viewer.") (base32 "1m33xsfwz0s8qi45lylagfllqg7fphf4dr0780rsvw75av9wk06h")))) (arguments `(#:tests? #f ;no "check" target + #:make-flags + (list "LIBCURSES=-lncurses") ,@(substitute-keyword-arguments (package-arguments samtools) - ((#:make-flags flags) - `(cons "LIBCURSES=-lncurses" ,flags)) ((#:phases phases) `(modify-phases ,phases (replace 'install @@ -5112,6 +5229,7 @@ viewer.") #t)))))) (inputs `(("perl" ,perl) + ("zlib:static" ,zlib "static") ("zlib" ,zlib))) (supported-systems '("x86_64-linux")) (home-page "https://github.com/wanpinglee/MOSAIK") @@ -5130,17 +5248,16 @@ Roche 454, Ion Torrent and Pacific BioSciences SMRT.") (define-public ngs-sdk (package (name "ngs-sdk") - (version "1.3.0") - (source - (origin - (method url-fetch) - (uri - (string-append "https://github.com/ncbi/ngs/archive/" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) - (sha256 - (base32 - "1wiyf4c6nm2j87pv015cbi0qny5byf3pbvcw3likifz5dl56ag40")))) + (version "2.9.3") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ncbi/ngs.git") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "17c0v1nah3g3d2ib5bbi0vhma1ghd6vb9xycavqsh64lhp840rk3")))) (build-system gnu-build-system) (arguments `(#:parallel-build? #f ; not supported @@ -5156,9 +5273,10 @@ Roche 454, Ion Torrent and Pacific BioSciences SMRT.") ;; The 'configure' script doesn't recognize things like ;; '--enable-fast-install'. - (zero? (system* "./configure" - (string-append "--build-prefix=" (getcwd) "/build") - (string-append "--prefix=" out)))))) + (invoke "./configure" + (string-append "--build-prefix=" (getcwd) "/build") + (string-append "--prefix=" out)) + #t))) (add-after 'unpack 'enter-dir (lambda _ (chdir "ngs-sdk") #t))))) (native-inputs `(("perl" ,perl))) @@ -5196,23 +5314,24 @@ simultaneously.") (define-public ncbi-vdb (package (name "ncbi-vdb") - (version "2.8.2") - (source - (origin - (method url-fetch) - (uri - (string-append "https://github.com/ncbi/ncbi-vdb/archive/" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) - (sha256 - (base32 - "1acn4bv81mfl137qnbn9995mjjhwd36pm0b7qli1iw5skrxa9j8m")))) + (version "2.9.3") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ncbi/ncbi-vdb.git") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1l4ny67nxwv1lagk9wwjbrgm7ln7adci6dnpc7k1yaln6shj0qpm")))) (build-system gnu-build-system) (arguments `(#:parallel-build? #f ; not supported #:tests? #f ; no "check" target #:phases (modify-phases %standard-phases + (add-after 'unpack 'make-files-writable + (lambda _ (for-each make-file-writable (find-files "." ".*")) #t)) (add-before 'configure 'set-perl-search-path (lambda _ ;; Work around "dotless @INC" build failure. @@ -5246,8 +5365,7 @@ simultaneously.") ;; The 'configure' script doesn't recognize things like ;; '--enable-fast-install'. - (zero? (system* - "./configure" + (invoke "./configure" (string-append "--build-prefix=" (getcwd) "/build") (string-append "--prefix=" (assoc-ref outputs "out")) (string-append "--debug") @@ -5256,7 +5374,8 @@ simultaneously.") (string-append "--with-ngs-sdk-prefix=" (assoc-ref inputs "ngs-sdk")) (string-append "--with-hdf5-prefix=" - (assoc-ref inputs "hdf5"))))))) + (assoc-ref inputs "hdf5"))) + #t))) (add-after 'install 'install-interfaces (lambda* (#:key outputs #:allow-other-keys) ;; Install interface libraries. On i686 the interface libraries @@ -5361,12 +5480,13 @@ subsequent visualization, annotation and storage of results.") (version "1.90b4") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/chrchang/plink-ng/archive/v" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/chrchang/plink-ng.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 - (base32 "09ixrds009aczjswxr2alcb774mksq5g0v78dgjjn1h4dky0kf9a")))) + (base32 "02npdwgkpfkdnhw819rhj5kw02a5k5m90b14zq9zzya4hyg929c0")))) (build-system gnu-build-system) (arguments '(#:tests? #f ;no "check" target @@ -5448,14 +5568,14 @@ structures, classes for genomic regions, mapped sequencing reads, etc.") (define-public preseq (package (name "preseq") - (version "2.0") + (version "2.0.3") (source (origin (method url-fetch) - (uri (string-append "https://github.com/smithlabcode/" - "preseq/archive/v" version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (uri (string-append "https://github.com/smithlabcode/preseq/" + "releases/download/v" version + "/preseq_v" version ".tar.bz2")) (sha256 - (base32 "08r684l50pnxjpvmhzjgqq56yv9rfw90k8vx0nsrnrzk8mf9hsdq")) + (base32 "149x9xmk1wy1gff85325yfzqc0qk4sgp1w6gbyj9cnji4x1dszbl")) (modules '((guix build utils))) (snippet '(begin ;; Remove bundled samtools. @@ -5498,25 +5618,38 @@ complexity samples.") (define-public python-screed (package (name "python-screed") - (version "0.9") + (version "1.0") (source (origin (method url-fetch) (uri (pypi-uri "screed" version)) (sha256 (base32 - "18czszp9fkx3j6jr7y5kp6dfialscgddk05mw1zkhh2zhn0jd8i0")))) + "148vcb7w2wr6a4w6vs2bsxanbqibxfk490zbcbg4m61s8669zdjx")))) (build-system python-build-system) (arguments - `(#:phases + '(#:phases (modify-phases %standard-phases - (replace 'check - (lambda _ - (setenv "PYTHONPATH" - (string-append (getenv "PYTHONPATH") ":.")) - (zero? (system* "nosetests" "--attr" "!known_failing"))))))) + ;; Tests must be run after installation, as the "screed" command does + ;; not exist right after building. + (delete 'check) + (add-after 'install 'check + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (setenv "PYTHONPATH" + (string-append out "/lib/python" + (string-take (string-take-right + (assoc-ref inputs "python") + 5) 3) + "/site-packages:" + (getenv "PYTHONPATH"))) + (setenv "PATH" (string-append out "/bin:" (getenv "PATH")))) + (invoke "python" "setup.py" "test") + #t))))) (native-inputs - `(("python-nose" ,python-nose))) + `(("python-pytest" ,python-pytest) + ("python-pytest-cov" ,python-pytest-cov) + ("python-pytest-runner" ,python-pytest-runner))) (inputs `(("python-bz2file" ,python-bz2file))) (home-page "https://github.com/dib-lab/screed/") @@ -5532,17 +5665,17 @@ sequence itself can be retrieved from these databases.") (define-public sra-tools (package (name "sra-tools") - (version "2.8.2-1") + (version "2.9.3") (source (origin - (method url-fetch) - (uri - (string-append "https://github.com/ncbi/sra-tools/archive/" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/ncbi/sra-tools.git") + (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 - "1camsijmvv2s45mb4iyf44ghl4gkd4rl0viphpcgl3ccchy32a0g")))) + "0663gcdxkziwsmlznjxysb00621rllpbz6jwsfifq7z3dj3lwm8b")))) (build-system gnu-build-system) (arguments `(#:parallel-build? #f ; not supported @@ -5592,8 +5725,7 @@ sequence itself can be retrieved from these databases.") ;; The 'configure' script doesn't recognize things like ;; '--enable-fast-install'. - (zero? (system* - "./configure" + (invoke "./configure" (string-append "--build-prefix=" (getcwd) "/build") (string-append "--prefix=" (assoc-ref outputs "out")) (string-append "--debug") @@ -5611,18 +5743,7 @@ sequence itself can be retrieved from these databases.") (string-append "--with-ngs-sdk-prefix=" (assoc-ref inputs "ngs-sdk")) (string-append "--with-hdf5-prefix=" - (assoc-ref inputs "hdf5")))))) - ;; This version of sra-tools fails to build with glibc because of a - ;; naming conflict. glibc-2.25/include/bits/mathcalls.h already - ;; contains a definition of "canonicalize", so we rename it. - ;; - ;; See upstream bug report: - ;; https://github.com/ncbi/sra-tools/issues/67 - (add-after 'unpack 'patch-away-glibc-conflict - (lambda _ - (substitute* "tools/bam-loader/bam.c" - (("canonicalize\\(" line) - (string-append "sra_tools_" line))) + (assoc-ref inputs "hdf5"))) #t))))) (native-inputs `(("perl" ,perl))) (inputs @@ -5643,14 +5764,15 @@ writing files into the .sra format.") (define-public seqan (package (name "seqan") - (version "1.4.2") + (version "2.4.0") (source (origin (method url-fetch) - (uri (string-append "http://packages.seqan.de/seqan-library/" - "seqan-library-" version ".tar.bz2")) + (uri (string-append "https://github.com/seqan/seqan/releases/" + "download/seqan-v" version + "/seqan-library-" version ".tar.xz")) (sha256 (base32 - "05s3wrrwn50f81aklfm65i4a749zag1vr8z03k21xm0pdxy47yvp")))) + "19a1rlxx03qy1i1iriicly68w64yjxbv24g9gdywnfmq998v35yx")))) ;; The documentation is 7.8MB and the includes are 3.6MB heavy, so it ;; makes sense to split the outputs. (outputs '("out" "doc")) @@ -5660,11 +5782,11 @@ writing files into the .sra format.") #:builder (begin (use-modules (guix build utils)) - (let ((tar (assoc-ref %build-inputs "tar")) - (bzip (assoc-ref %build-inputs "bzip2")) - (out (assoc-ref %outputs "out")) - (doc (assoc-ref %outputs "doc"))) - (setenv "PATH" (string-append tar "/bin:" bzip "/bin")) + (let ((tar (assoc-ref %build-inputs "tar")) + (xz (assoc-ref %build-inputs "xz")) + (out (assoc-ref %outputs "out")) + (doc (assoc-ref %outputs "doc"))) + (setenv "PATH" (string-append tar "/bin:" xz "/bin")) (invoke "tar" "xvf" (assoc-ref %build-inputs "source")) (chdir (string-append "seqan-library-" ,version)) (copy-recursively "include" (string-append out "/include")) @@ -5673,7 +5795,7 @@ writing files into the .sra format.") (native-inputs `(("source" ,source) ("tar" ,tar) - ("bzip2" ,bzip2))) + ("xz" ,xz))) (home-page "http://www.seqan.de") (synopsis "Library for nucleotide sequence analysis") (description @@ -5684,6 +5806,41 @@ manipulation, online and indexed string search, efficient I/O of bioinformatics file formats, sequence alignment, and more.") (license license:bsd-3))) +(define-public seqan-1 + (package (inherit seqan) + (name "seqan") + (version "1.4.2") + (source (origin + (method url-fetch) + (uri (string-append "http://packages.seqan.de/seqan-library/" + "seqan-library-" version ".tar.bz2")) + (sha256 + (base32 + "05s3wrrwn50f81aklfm65i4a749zag1vr8z03k21xm0pdxy47yvp")))) + ;; The documentation is 7.8MB and the includes are 3.6MB heavy, so it + ;; makes sense to split the outputs. + (outputs '("out" "doc")) + (build-system trivial-build-system) + (arguments + `(#:modules ((guix build utils)) + #:builder + (begin + (use-modules (guix build utils)) + (let ((tar (assoc-ref %build-inputs "tar")) + (bzip (assoc-ref %build-inputs "bzip2")) + (out (assoc-ref %outputs "out")) + (doc (assoc-ref %outputs "doc"))) + (setenv "PATH" (string-append tar "/bin:" bzip "/bin")) + (invoke "tar" "xvf" (assoc-ref %build-inputs "source")) + (chdir (string-append "seqan-library-" ,version)) + (copy-recursively "include" (string-append out "/include")) + (copy-recursively "share" (string-append doc "/share")) + #t)))) + (native-inputs + `(("source" ,source) + ("tar" ,tar) + ("bzip2" ,bzip2))))) + (define-public seqmagick (package (name "seqmagick") @@ -5713,24 +5870,16 @@ is one that takes arguments.") (define-public seqtk (package (name "seqtk") - (version "1.2") + (version "1.3") (source (origin - (method url-fetch) - (uri (string-append - "https://github.com/lh3/seqtk/archive/v" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/lh3/seqtk.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "0ywdyzpmfiz2wp6ampbzqg4y8bj450nfgqarpamg045b8mk32lxx")) - (modules '((guix build utils))) - (snippet - '(begin - ;; Remove extraneous header files, as is done in the seqtk - ;; master branch. - (for-each (lambda (file) (delete-file file)) - (list "ksort.h" "kstring.h" "kvec.h")) - #t)))) + "1bfzlqa84b5s1qi22blmmw2s8xdyp9h9ydcq22pfjhh5gab3yz6l")))) (build-system gnu-build-system) (arguments `(#:phases @@ -5738,11 +5887,12 @@ is one that takes arguments.") (delete 'configure) (replace 'check ;; There are no tests, so we just run a sanity check. - (lambda _ (zero? (system* "./seqtk" "seq")))) + (lambda _ (invoke "./seqtk" "seq") #t)) (replace 'install (lambda* (#:key outputs #:allow-other-keys) (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) - (install-file "seqtk" bin))))))) + (install-file "seqtk" bin) + #t)))))) (inputs `(("zlib" ,zlib))) (home-page "https://github.com/lh3/seqtk") @@ -5758,20 +5908,20 @@ optionally compressed by gzip.") (name "snap-aligner") (version "1.0beta.18") (source (origin - (method url-fetch) - (uri (string-append - "https://github.com/amplab/snap/archive/v" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/amplab/snap.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "1vnsjwv007k1fl1q7d681kbwn6bc66cgw6h16hym6gvyy71qv2ly")))) + "01w3qq4wm07z73vky0cfwlmrbf50n3w722cxrlzxfi99mnb808d8")))) (build-system gnu-build-system) (arguments '(#:phases (modify-phases %standard-phases (delete 'configure) - (replace 'check (lambda _ (zero? (system* "./unit_tests")))) + (replace 'check (lambda _ (invoke "./unit_tests") #t)) (replace 'install (lambda* (#:key outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) @@ -5800,14 +5950,14 @@ of these reads to align data quickly through a hash-based indexing scheme.") (version "2.1b") (source (origin - (method url-fetch) - (uri (string-append - "https://github.com/biocore/sortmerna/archive/" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/biocore/sortmerna.git") + (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 - "1ghaghvd82af9j5adavxh77g7hm247d1r69m3fbi6f1jdivj5ldk")))) + "0j3mbz4n25738yijmjbr5r4fyvkgm8v5vn3sshyfvmyqf5q9byqf")))) (build-system gnu-build-system) (outputs '("out" ;for binaries "db")) ;for sequence databases @@ -5877,7 +6027,8 @@ application of SortMeRNA is filtering rRNA from metatranscriptomic data.") (lambda _ (substitute* "Makefile" (("(COMPILATION_TIME_PLACE=\")(.*)(\")" _ pre mid post) - (string-append pre "Built with Guix" post))))) + (string-append pre "Built with Guix" post))) + #t)) (add-after 'enter-source-dir 'do-not-use-bundled-htslib (lambda _ (substitute* "Makefile" @@ -5961,7 +6112,8 @@ sequences.") (lambda* (#:key outputs #:allow-other-keys) (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) (mkdir-p bin) - (copy-recursively "../bin" bin)))) + (copy-recursively "../bin" bin)) + #t)) ;; no "configure" script (delete 'configure)))) (inputs `(("zlib" ,zlib))) @@ -6053,8 +6205,7 @@ Cuffdiff or Ballgown programs.") #:phases (modify-phases %standard-phases (replace 'check - (lambda _ - (zero? (system* "python" "-m" "unittest" "discover" "-v"))))))) + (lambda _ (invoke "python" "-m" "unittest" "discover" "-v") #t))))) (propagated-inputs `(("python-sqlalchemy" ,python2-sqlalchemy) ("python-decorator" ,python2-decorator) @@ -6165,14 +6316,14 @@ information as possible.") (define-public r-vegan (package (name "r-vegan") - (version "2.5-2") + (version "2.5-3") (source (origin (method url-fetch) (uri (cran-uri "vegan" version)) (sha256 (base32 - "13pyqvlpz64qibi8k5d109v7q09j06mbv6ndix3n4cn21mjx391c")))) + "023xznh0iy0496icpchadmp7a3rk3nj9s48fvwlvp3dssw58yp3c")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) @@ -6195,14 +6346,14 @@ data types as well.") (define-public r-annotate (package (name "r-annotate") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotate" version)) (sha256 (base32 - "1qmncyvy147a1ll3iri45p822kcs3s7583jfnq9jf6sz9ilk8cjf")))) + "0p6c96lay23a67dyirgnwzm2yw22m592z780vy6p4nqwla8ha18n")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -6222,13 +6373,13 @@ microarrays.") (define-public r-copynumber (package (name "r-copynumber") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "copynumber" version)) (sha256 (base32 - "0y9nnwb0psphp3ix88wj2f8z5gr45r5znf55w892ysm27isdpmms")))) + "0ipwj9i5p1bwhg5d80jdjagm02krpj2v0j47qdgw41h8wncdyal3")))) (build-system r-build-system) (propagated-inputs `(("r-s4vectors" ,r-s4vectors) @@ -6245,14 +6396,14 @@ penalized least squares regression method.") (define-public r-geneplotter (package (name "r-geneplotter") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "geneplotter" version)) (sha256 (base32 - "055g28xgiazl4l0gkg8xiamks64f5yckjjyvw1abd6d6qjavwx0g")))) + "10khr0pznxf3m0f5gzck9ymljrwcv3vamfmpskd51yjh36lhllqz")))) (build-system r-build-system) (propagated-inputs `(("r-annotate" ,r-annotate) @@ -6270,14 +6421,14 @@ penalized least squares regression method.") (define-public r-genefilter (package (name "r-genefilter") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "genefilter" version)) (sha256 (base32 - "14l0ff02spmjwxj0m1czhg5vlkgwcfi73cym8m2n9vn6i7bjdaqi")))) + "0p64s1n1627yafnp25wjr4b22p34lqw574fx2qg4s1m0lffh1z6i")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) @@ -6297,14 +6448,14 @@ high-throughput sequencing experiments.") (define-public r-deseq2 (package (name "r-deseq2") - (version "1.20.0") + (version "1.22.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DESeq2" version)) (sha256 (base32 - "1wjnfpb41a9mmf9a22bz4zh7r1d4id50vpdc1mn5vfzrz7li9qik")))) + "1b2bmvcsfzvks47d7w46zplcwz0kgcdhx5xmx3x9lp2gvx2p84r5")))) (properties `((upstream-name . "DESeq2"))) (build-system r-build-system) (propagated-inputs @@ -6334,14 +6485,14 @@ distribution.") (define-public r-dexseq (package (name "r-dexseq") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DEXSeq" version)) (sha256 (base32 - "1mqb3mdxcsi3largsl7k27bvqrgps9ixv806xvmf29pw0xn05sg1")))) + "0jh1640cnzpk8x3155cqc8dvrs1rciw3d6nv2k70baw96bhrynp8")))) (properties `((upstream-name . "DEXSeq"))) (build-system r-build-system) (propagated-inputs @@ -6377,14 +6528,14 @@ exploration of the results.") (define-public r-annotationforge (package (name "r-annotationforge") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationForge" version)) (sha256 (base32 - "12ffj7h95adiya5mzyjxazqn1qgr434ajpabfcyhrj5v83s4vk65")))) + "13yvhf3yskmvhs8szs6rkw93h81h5xqa3h19h91pp6nprhc8s3ll")))) (properties `((upstream-name . "AnnotationForge"))) (build-system r-build-system) @@ -6407,14 +6558,14 @@ databases. Packages produced are intended to be used with AnnotationDbi.") (define-public r-rbgl (package (name "r-rbgl") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RBGL" version)) (sha256 (base32 - "0hj972mmqpyi5fx1rq33kysavdyz4nspi6gcffzi3rv339m0anhf")))) + "0jy95m38c4qp0a12097hhm2gg63k96k6ydhb11dy379h3ziapcar")))) (properties `((upstream-name . "RBGL"))) (build-system r-build-system) (propagated-inputs `(("r-graph" ,r-graph))) @@ -6428,14 +6579,14 @@ the graph algorithms contained in the Boost library.") (define-public r-gseabase (package (name "r-gseabase") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GSEABase" version)) (sha256 (base32 - "11bv92svik399q677jv96b71i4bq68xxyxn1yijpdik2lq4hgl7a")))) + "110al7x0ig8plzrprvhwc7xshi1jzpj2n8llhhg2fh6v6k0k6awr")))) (properties `((upstream-name . "GSEABase"))) (build-system r-build-system) (propagated-inputs @@ -6455,14 +6606,14 @@ Enrichment Analysis} (GSEA).") (define-public r-category (package (name "r-category") - (version "2.46.0") + (version "2.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Category" version)) (sha256 (base32 - "03wfqa8d1dgwsm327zl2mpkq7dq3mzhq12598qz3ylfhrwplbgx0")))) + "1jdm83bwdfhpfm1y6hwgvxzj6l83h1bdkqv23799kzywnwm016kv")))) (properties `((upstream-name . "Category"))) (build-system r-build-system) (propagated-inputs @@ -6486,14 +6637,14 @@ analysis.") (define-public r-gostats (package (name "r-gostats") - (version "2.46.0") + (version "2.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOstats" version)) (sha256 (base32 - "1i5mydz5d95w2k28qr9j01hmbnl2id55jq94jvcpcyp1pvinkdq0")))) + "0wlqqgfynwqnqhckhsfjwg9zkj6hkmzwd5y76dhqz720vy21rcln")))) (properties `((upstream-name . "GOstats"))) (build-system r-build-system) (propagated-inputs @@ -6517,14 +6668,14 @@ testing and other simple calculations.") (define-public r-shortread (package (name "r-shortread") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ShortRead" version)) (sha256 (base32 - "038z3z7qaw5bpgjzy91sjkybsny6jwjjsrnnq4gdqdw9ss1qy1fb")))) + "0iks123i1adkb9i2q4wvfqdmmj9dy867jvngj9757y8gj6xbcpy1")))) (properties `((upstream-name . "ShortRead"))) (build-system r-build-system) (inputs @@ -6559,14 +6710,14 @@ ungapped alignment formats.") (define-public r-systempiper (package (name "r-systempiper") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "systemPipeR" version)) (sha256 (base32 - "1550pd63mmky0vgkmpni7zf14kqz1741wv63nfaw29kcmhh3m5lm")))) + "0l26q8zjdmzg84g7f25gv9z60sykybahlpg5bg9bmpbg5lzcsx04")))) (properties `((upstream-name . "systemPipeR"))) (build-system r-build-system) (propagated-inputs @@ -6605,14 +6756,14 @@ annotation infrastructure.") (define-public r-grohmm (package (name "r-grohmm") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "groHMM" version)) (sha256 (base32 - "1kjb14apyly44qdlx2ld6gr69wlazd4mbhs58l35hir12aphgrzp")))) + "1ph92fv44b90v7mk4b1mjvv0dlrhl8ba01klxbnd0vs4qn9zxplh")))) (properties `((upstream-name . "groHMM"))) (build-system r-build-system) (propagated-inputs @@ -6687,17 +6838,17 @@ SELECT or UPDATE queries to an end-point.") (define-public vsearch (package (name "vsearch") - (version "2.8.0") + (version "2.9.1") (source (origin - (method url-fetch) - (uri (string-append - "https://github.com/torognes/vsearch/archive/v" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/torognes/vsearch.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "15pbirgzhvflj4pi5n82vybbzjy9mlb0lv5l3qhrmdkfzpbyahw3")) + "0vhrpjfdf75ba04b24xknp41790cvcgwl0vgpy7qbzj5xh2521ss")) (patches (search-patches "vsearch-unbundle-cityhash.patch")) (snippet '(begin @@ -6708,11 +6859,6 @@ SELECT or UPDATE queries to an end-point.") (delete-file "src/city.cc") #t)))) (build-system gnu-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'autogen - (lambda _ (zero? (system* "autoreconf" "-vif"))))))) (inputs `(("zlib" ,zlib) ("bzip2" ,bzip2) @@ -6855,14 +7001,14 @@ generate FASTA, JSON, YAML, RDF, JSON-LD, HTML, CSV, tabular output etc.") (define-public bioruby (package (name "bioruby") - (version "1.5.1") + (version "1.5.2") (source (origin (method url-fetch) (uri (rubygems-uri "bio" version)) (sha256 (base32 - "0hdl0789c9n4mprnx5pgd46bfwl8d000rqpamj5h6kkjgspijv49")))) + "1d56amdsjv1mag7m6gv2w0xij8hqx1v5xbdjsix8sp3yp36m7938")))) (build-system ruby-build-system) (propagated-inputs `(("ruby-libxml" ,ruby-libxml))) @@ -6924,13 +7070,13 @@ barplots or heatmaps.") (define-public r-biocgenerics (package (name "r-biocgenerics") - (version "0.26.0") + (version "0.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocGenerics" version)) (sha256 (base32 - "19qxhy2cd3pykkhzbb5q3crgaxf65cpzf2mkfsz16gqhi8flj72p")))) + "0cvpsrhg7sn7lpqgxvqrsagv6j7xj5rafq5xdjfd8zc4gxrs5rb8")))) (properties `((upstream-name . "BiocGenerics"))) (build-system r-build-system) @@ -6944,13 +7090,13 @@ packages.") (define-public r-biocinstaller (package (name "r-biocinstaller") - (version "1.30.0") + (version "1.32.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocInstaller" version)) (sha256 (base32 - "1xg1gi1hf5vflp71ji21gnmr4kcjpx8a6c47cllpc7yqnjv5nfg0")))) + "1s1f9qhyf3mc73ir25x2zlgi9hf45a37lg4z8fbva4i21hqisgsl")))) (properties `((upstream-name . "BiocInstaller"))) (build-system r-build-system) @@ -6963,13 +7109,13 @@ Bioconductor, CRAN, and Github.") (define-public r-biocviews (package (name "r-biocviews") - (version "1.48.2") + (version "1.50.5") (source (origin (method url-fetch) (uri (bioconductor-uri "biocViews" version)) (sha256 (base32 - "01yiafayl1m5704xdd2cn3zjc78rs10dqyz66lr3qkf6d8w66938")))) + "0rc1n89n04ylvy9gvsgvizcs77bh70jg1nkjjsjs7rqbr3zzdysz")))) (properties `((upstream-name . "biocViews"))) (build-system r-build-system) @@ -7013,19 +7159,20 @@ authoring books and technical documents with R Markdown.") (define-public r-biocstyle (package - (name "r-biocstyle") - (version "2.8.2") + (name "r-biocstyle") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocStyle" version)) (sha256 (base32 - "17m901ylz00w1a3nq5f910v55zixm1nr6rb3qrsbhqd94qzr0l2p")))) + "01lm8xljilj666fcl3wnw82dxkcxnlr294lddr553rm8xr5nwg31")))) (properties `((upstream-name . "BiocStyle"))) (build-system r-build-system) (propagated-inputs - `(("r-bookdown" ,r-bookdown) + `(("r-biocmanager" ,r-biocmanager) + ("r-bookdown" ,r-bookdown) ("r-knitr" ,r-knitr) ("r-rmarkdown" ,r-rmarkdown) ("r-yaml" ,r-yaml))) @@ -7039,13 +7186,13 @@ functionality.") (define-public r-bioccheck (package (name "r-bioccheck") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocCheck" version)) (sha256 (base32 - "1srp1g809f1nn0fyqknr7r6dq89bw1xpjvmygr7cw6ffknbc671s")))) + "0zamvs5jar38293ff27imvwy0ra25y64ls9z8w3q1y4jcp8p8pg7")))) (properties `((upstream-name . "BiocCheck"))) (build-system r-build-system) @@ -7072,8 +7219,9 @@ functionality.") `(("r-codetools" ,r-codetools) ("r-graph" ,r-graph) ("r-httr" ,r-httr) + ("r-knitr" ,r-knitr) ("r-optparse" ,r-optparse) - ("r-biocinstaller" ,r-biocinstaller) + ("r-biocmanager" ,r-biocmanager) ("r-biocviews" ,r-biocviews) ("r-stringdist" ,r-stringdist))) (home-page "https://bioconductor.org/packages/BiocCheck") @@ -7108,13 +7256,13 @@ that accept short and long options.") (define-public r-dnacopy (package (name "r-dnacopy") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DNAcopy" version)) (sha256 (base32 - "03hfhmmc5y60r2gcgm367w2fr7qj115l74m9bp3h9qpn5yci0d8n")))) + "04cqdqxhva66xwh1s2vffi56b9fcrqd4slcrvqasj5lp2rkjli82")))) (properties `((upstream-name . "DNAcopy"))) (build-system r-build-system) @@ -7130,13 +7278,13 @@ abnormal copy number.") (define-public r-s4vectors (package (name "r-s4vectors") - (version "0.18.3") + (version "0.20.1") (source (origin (method url-fetch) (uri (bioconductor-uri "S4Vectors" version)) (sha256 (base32 - "02bps2rpjqx2npwxq3x62ncwi9ggr165cwi56h6hld28bw2gddy8")))) + "18whrw67nxn82xshckl2pjy7d14sa3c27h3n9naqyqwz88lr6dzg")))) (properties `((upstream-name . "S4Vectors"))) (build-system r-build-system) @@ -7182,13 +7330,13 @@ utilities for sequence data management under the ACNUC system.") (define-public r-iranges (package (name "r-iranges") - (version "2.14.10") + (version "2.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IRanges" version)) (sha256 (base32 - "10ccw930vfmkskkrzbps14xglqlkxf588623dr7f1a9ckx7yr2p6")))) + "0ljppsk611xi72gc8mbdx1311b63b1ijd401jz5xmxk5frla1nc1")))) (properties `((upstream-name . "IRanges"))) (build-system r-build-system) @@ -7211,7 +7359,7 @@ possible.") (define-public r-genomeinfodbdata (package (name "r-genomeinfodbdata") - (version "0.99.1") + (version "1.2.0") (source (origin (method url-fetch) ;; We cannot use bioconductor-uri here because this tarball is @@ -7221,7 +7369,7 @@ possible.") version ".tar.gz")) (sha256 (base32 - "0hipipvyvrh75n68hsjg35sxbcfzrghzxv547vnkk2f8ya99g01r")))) + "0di6nlqpsyqf693k2na65ayqldih563x3zfrczpqc5q2hl5kg35c")))) (properties `((upstream-name . "GenomeInfoDbData"))) (build-system r-build-system) @@ -7234,13 +7382,13 @@ ID and species. It is used by functions in the GenomeInfoDb package.") (define-public r-genomeinfodb (package (name "r-genomeinfodb") - (version "1.16.0") + (version "1.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeInfoDb" version)) (sha256 (base32 - "0yhnqhaydmmq7ihmhj3rbal4afq5p993l2qqrd0n5wmbyg7glg2d")))) + "049pyzr8iszv3g7wdqf3pz7vg7bzd450c20ln6fgw4g5xnkkr10s")))) (properties `((upstream-name . "GenomeInfoDb"))) (build-system r-build-system) @@ -7262,13 +7410,13 @@ names in their natural, rather than lexicographic, order.") (define-public r-edger (package (name "r-edger") - (version "3.22.2") + (version "3.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "edgeR" version)) (sha256 (base32 - "07py2g6vg9jbflwhc1hnzr2silbinrjwxq3mkq30nzjgf0n0hrf3")))) + "0ihihgzrgb4q3xc8xkzp1v76ndgihrj4gas00fa25vggfs1v6hvg")))) (properties `((upstream-name . "edgeR"))) (build-system r-build-system) (propagated-inputs @@ -7290,13 +7438,13 @@ CAGE.") (define-public r-variantannotation (package (name "r-variantannotation") - (version "1.26.0") + (version "1.28.1") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantAnnotation" version)) (sha256 (base32 - "06bccdf57vja7m63chmgc4539lwng3q3b8zxn285fj8524l6mcn7")))) + "0gvah258mkaafhbna81zwknx8qr3lidbcx5qvwk39q3yswr9mi49")))) (properties `((upstream-name . "VariantAnnotation"))) (inputs @@ -7328,13 +7476,13 @@ coding changes and predict coding outcomes.") (define-public r-limma (package (name "r-limma") - (version "3.36.1") + (version "3.38.2") (source (origin (method url-fetch) (uri (bioconductor-uri "limma" version)) (sha256 (base32 - "1982g5v35ilfgxm2vkq1p3j1bbir795pjvfzx4nzam2rlqqymbqm")))) + "1wkh362rmn24q7bkinb6nx62a31wl3r3myg5l326gx65wpwdnx97")))) (build-system r-build-system) (home-page "http://bioinf.wehi.edu.au/limma") (synopsis "Package for linear models for microarray and RNA-seq data") @@ -7347,13 +7495,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.") (define-public r-xvector (package (name "r-xvector") - (version "0.20.0") + (version "0.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "XVector" version)) (sha256 (base32 - "1zjlhh9lsyhg0js1858csyw2389kbrzdqnqnha833wazkwxilp3f")))) + "01fph1ydd6g0rl5mcw54spx22glq2kqv7wyw8bqw0plmabzcwwdm")))) (properties `((upstream-name . "XVector"))) (build-system r-build-system) @@ -7383,13 +7531,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.") (define-public r-genomicranges (package (name "r-genomicranges") - (version "1.32.3") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicRanges" version)) (sha256 (base32 - "03gmka6rlz18vd4229796l5l3l6446v5cb90sn2nb5knjbp84hni")))) + "0bgh14d15dpf2iy36qinw45r6n45rqkf0ghazrdl3jfva6vbrb29")))) (properties `((upstream-name . "GenomicRanges"))) (build-system r-build-system) @@ -7412,13 +7560,13 @@ manipulating genomic intervals and variables defined along a genome.") (define-public r-biobase (package (name "r-biobase") - (version "2.40.0") + (version "2.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Biobase" version)) (sha256 (base32 - "1iwds2a5ir29k19dbpynlc7nn836cw2gamchhgpi2jf2xar9m9jz")))) + "10nr6nrkj5vlq8hsgbhbhv669z0dbpz4m3vz9k32rx1czbrrqwin")))) (properties `((upstream-name . "Biobase"))) (build-system r-build-system) @@ -7434,13 +7582,13 @@ on Bioconductor or which replace R functions.") (define-public r-annotationdbi (package (name "r-annotationdbi") - (version "1.42.1") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationDbi" version)) (sha256 (base32 - "0afkbzli08vq02r2pr9phrz3rxd6ilp1w7yw8y99nbjiz14f8b1c")))) + "1954vimkx5yb9irppq8vssq0f3yjkg36w38b9r0rqmijx1ps7x5d")))) (properties `((upstream-name . "AnnotationDbi"))) (build-system r-build-system) @@ -7461,13 +7609,13 @@ annotation data packages using SQLite data storage.") (define-public r-biomart (package (name "r-biomart") - (version "2.36.1") + (version "2.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biomaRt" version)) (sha256 (base32 - "0b70s350ffc74v3xz5c3jpazr9zxdb7gjmjfj7aghlsrizrspill")))) + "1lshkknp7dmr3p6dd2zbv86cc71h53ggh9ji83jcjym8sgbbspl2")))) (properties `((upstream-name . "biomaRt"))) (build-system r-build-system) @@ -7494,13 +7642,13 @@ powerful online queries from gene annotation to database mining.") (define-public r-biocparallel (package (name "r-biocparallel") - (version "1.14.1") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocParallel" version)) (sha256 (base32 - "00qg1kg2l9qqpyjaw5q910cmf84vwfiw1fhsx3ig784gwinwgj6n")))) + "0g16cy0vjapqkb188z63r1b6y96m9g8vx0a3v2qavzxc177k0cja")))) (properties `((upstream-name . "BiocParallel"))) (build-system r-build-system) @@ -7519,13 +7667,13 @@ objects.") (define-public r-biostrings (package (name "r-biostrings") - (version "2.48.0") + (version "2.50.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Biostrings" version)) (sha256 (base32 - "118b490jk87ydigm6ln25ms4kskzkw0akmh77clzznhzpqnxsi6j")))) + "1qyv1ps7vy6gy78pm2rcikg0bgf1mv7falahjp3pkwqq1272hrl8")))) (properties `((upstream-name . "Biostrings"))) (build-system r-build-system) @@ -7545,13 +7693,13 @@ biological sequences or sets of sequences.") (define-public r-rsamtools (package (name "r-rsamtools") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsamtools" version)) (sha256 (base32 - "1s65y5wn4d0x8zsljg2kmhcl6r9884h95kr041j7hp49bmxg3an6")))) + "01v4bjhj2i126pwyk0v9lvmfp2ih495xsq903k3xa2z24bjxphbi")))) (properties `((upstream-name . "Rsamtools"))) (build-system r-build-system) @@ -7589,13 +7737,13 @@ files.") (define-public r-delayedarray (package (name "r-delayedarray") - (version "0.6.1") + (version "0.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedArray" version)) (sha256 (base32 - "0sjwszxdi0vkj2i2di5i46gh9chc660yr3gs5nk9qnqp77713zds")))) + "0cl5anqkjwvqx19snjhz0zj8cp8ibckiifl28h821h50g62nvb2f")))) (properties `((upstream-name . "DelayedArray"))) (build-system r-build-system) @@ -7620,13 +7768,13 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns), (define-public r-summarizedexperiment (package (name "r-summarizedexperiment") - (version "1.10.1") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SummarizedExperiment" version)) (sha256 (base32 - "0v3zxl9cqsv79ag5cnvzlhvgaz5cr8f4rn7flmwnwpqd508cznl1")))) + "07805572xhpj5mfwq6kw1ha21wgalqvhh4ydvafyl1bnf3r20vps")))) (properties `((upstream-name . "SummarizedExperiment"))) (build-system r-build-system) @@ -7651,13 +7799,13 @@ samples.") (define-public r-genomicalignments (package (name "r-genomicalignments") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicAlignments" version)) (sha256 (base32 - "00pi2cnkkbj2023fg2x2cmglkdalwzy1vr3glsikwz7ix9yylcaw")))) + "0a3zhwripfw2508fvgx3wzqa8nq8vnslg97a911znpwvxh53jl24")))) (properties `((upstream-name . "GenomicAlignments"))) (build-system r-build-system) @@ -7684,13 +7832,13 @@ alignments.") (define-public r-rtracklayer (package (name "r-rtracklayer") - (version "1.40.3") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rtracklayer" version)) (sha256 (base32 - "0kvsjdaypn1jnxbnsxpycildwdyxwnjkigfq8qm8mlyfc4ahdgy3")))) + "0a4mhd926w9slkfil5xgngjsfdj024a4w57w2bm3d4r0pj8y5da7")))) (build-system r-build-system) (arguments `(#:phases @@ -7731,13 +7879,13 @@ as well as query and modify the browser state, such as the current viewport.") (define-public r-genomicfeatures (package (name "r-genomicfeatures") - (version "1.32.0") + (version "1.34.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFeatures" version)) (sha256 (base32 - "1cqcl72q0k5wylw1brn4g4h7xzys1v06piry19cvp0gjcvm5sp7a")))) + "0slq6hv5bmc3bgrl824jzmr6db3fvaj6b7ihwmdn76pgqqbq2fq6")))) (properties `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) @@ -7772,7 +7920,7 @@ extracting the desired features in a convenient format.") (define-public r-go-db (package (name "r-go-db") - (version "3.5.0") + (version "3.7.0") (source (origin (method url-fetch) (uri (string-append "https://www.bioconductor.org/packages/" @@ -7780,7 +7928,7 @@ extracting the desired features in a convenient format.") version ".tar.gz")) (sha256 (base32 - "02d1mn1al3q7qvhx1ylrr3ar4w4iw0qyi5d89v2336rzwk9maq35")))) + "0i3wcf5h3n0dawzc1hy0kv74f06j80c47n4p3g3fmrcxlhi3jpa5")))) (properties `((upstream-name . "GO.db"))) (build-system r-build-system) @@ -7793,35 +7941,16 @@ extracting the desired features in a convenient format.") information about the latest version of the Gene Ontologies.") (license license:artistic2.0))) -(define-public r-graph - (package - (name "r-graph") - (version "1.58.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "graph" version)) - (sha256 - (base32 - "1zx445lk36g1s6i5dbhhf00nzzazyklfjxxjfax6q8hnhvgm9759")))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics))) - (home-page "https://bioconductor.org/packages/graph") - (synopsis "Handle graph data structures in R") - (description - "This package implements some simple graph handling capabilities for R.") - (license license:artistic2.0))) - (define-public r-topgo (package (name "r-topgo") - (version "2.32.0") + (version "2.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "topGO" version)) (sha256 (base32 - "05yxnkid8bgw9lkm90if9fg63djhgvbailfa3qsfqa5c0zjmixw1")))) + "1j1jcd16j564kr6qz28140fzmnh9xasi84v1c1fi98sqv30zq9bh")))) (properties `((upstream-name . "topGO"))) (build-system r-build-system) @@ -7848,13 +7977,13 @@ dependencies between GO terms can be implemented and applied.") (define-public r-bsgenome (package (name "r-bsgenome") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BSgenome" version)) (sha256 (base32 - "1rk2piqq5dppkd51ln3r872d7ng3rvq98071mnd0xdv2xwnyn5g8")))) + "07z4zxx0khrc86qqvc7vxww8df9fh6pyks9ajxkc9gdqr5nn79j7")))) (properties `((upstream-name . "BSgenome"))) (build-system r-build-system) @@ -7909,13 +8038,13 @@ genome data packages and support for efficient SNP representation.") (define-public r-impute (package (name "r-impute") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "impute" version)) (sha256 (base32 - "1d3cpfaqlq2gnb3hsc2yhxwkrnbd7m6ifif32yp0ya0jr5brl4hr")))) + "08z0pj1dz5iq967nwj67qyka7ir7m5an2ggv7bsrlz3apzfsla33")))) (inputs `(("gfortran" ,gfortran))) (build-system r-build-system) @@ -7929,13 +8058,13 @@ microarray data, using nearest neighbor averaging.") (define-public r-seqpattern (package (name "r-seqpattern") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqPattern" version)) (sha256 (base32 - "0dw0yldfcf0ibvpqxlpx1ijnjf9lma47w9w22siszzhw09i0wp3w")))) + "0di83qi83mrlw7i12khsq55d03hlazcywaa9m9pki1sfhafpq733")))) (properties `((upstream-name . "seqPattern"))) (build-system r-build-system) @@ -7956,13 +8085,13 @@ reference point and sorted by a user defined feature.") (define-public r-genomation (package (name "r-genomation") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "genomation" version)) (sha256 (base32 - "1vdmdyrq0n7pf8cvy2950v7hrcrcbd9zl4fg7dcmyly3iiwdyirp")))) + "0g0v4alfpqlinqinjnyzl3mrjnpbdx9ri34mcaiqbvbvg8ic8wvg")))) (build-system r-build-system) (propagated-inputs `(("r-biostrings" ,r-biostrings) @@ -8002,7 +8131,7 @@ genomic intervals. In addition, it can use BAM or BigWig files as input.") (define-public r-genomationdata (package (name "r-genomationdata") - (version "1.10.0") + (version "1.14.0") (source (origin (method url-fetch) ;; We cannot use bioconductor-uri here because this tarball is @@ -8012,7 +8141,7 @@ genomic intervals. In addition, it can use BAM or BigWig files as input.") "genomationData_" version ".tar.gz")) (sha256 (base32 - "0h7g5x3kyb50qlblz5hc85lfm6n6f5nb68i146way3ggs04sqvla")))) + "10xyb8akjrhmak2i0mnv1agny2ipy364q9nlibyplpzc7vdb6bw7")))) (build-system r-build-system) ;; As this package provides little more than large data files, it doesn't ;; make sense to build substitutes. @@ -8030,7 +8159,7 @@ downloaded from Encode.") (define-public r-org-hs-eg-db (package (name "r-org-hs-eg-db") - (version "3.5.0") + (version "3.7.0") (source (origin (method url-fetch) ;; We cannot use bioconductor-uri here because this tarball is @@ -8040,7 +8169,7 @@ downloaded from Encode.") "org.Hs.eg.db_" version ".tar.gz")) (sha256 (base32 - "1v6wa5613cjq59xd7x1qz8lr9nb2abm9abl2cci1khrnrlpla927")))) + "1qxz9l80yg3qdqszs6dsscp7lrpfi1bgd0pxh9j7q34vprzwhdim")))) (properties `((upstream-name . "org.Hs.eg.db"))) (build-system r-build-system) @@ -8056,7 +8185,7 @@ on mapping using Entrez Gene identifiers.") (define-public r-org-ce-eg-db (package (name "r-org-ce-eg-db") - (version "3.5.0") + (version "3.7.0") (source (origin (method url-fetch) ;; We cannot use bioconductor-uri here because this tarball is @@ -8066,7 +8195,7 @@ on mapping using Entrez Gene identifiers.") "org.Ce.eg.db_" version ".tar.gz")) (sha256 (base32 - "02ggchixlmzywhsbr0h2ms4dravv7m5964cjxqcjxqs16vjwlbk9")))) + "1w5br1ss4ha8wv4v2saj7cmbjc2jw0dyj2f2y269l078z31wcnaz")))) (properties `((upstream-name . "org.Ce.eg.db"))) (build-system r-build-system) @@ -8082,7 +8211,7 @@ annotations for the genome of the model worm Caenorhabditis elegans.") (define-public r-org-dm-eg-db (package (name "r-org-dm-eg-db") - (version "3.5.0") + (version "3.7.0") (source (origin (method url-fetch) ;; We cannot use bioconductor-uri here because this tarball is @@ -8092,7 +8221,7 @@ annotations for the genome of the model worm Caenorhabditis elegans.") "org.Dm.eg.db_" version ".tar.gz")) (sha256 (base32 - "033qak1d3wwz17va0bh8z8p8arx0aw2va6gm1qfwsvdkj9cd9d7d")))) + "1pqjrzlyg72bjpy8zsxvaglc7jsv176bnyi87xdajmkvsgxpm7b3")))) (properties `((upstream-name . "org.Dm.eg.db"))) (build-system r-build-system) @@ -8108,7 +8237,7 @@ annotations for the genome of the model fruit fly Drosophila melanogaster.") (define-public r-org-mm-eg-db (package (name "r-org-mm-eg-db") - (version "3.5.0") + (version "3.7.0") (source (origin (method url-fetch) ;; We cannot use bioconductor-uri here because this tarball is @@ -8118,7 +8247,7 @@ annotations for the genome of the model fruit fly Drosophila melanogaster.") "org.Mm.eg.db_" version ".tar.gz")) (sha256 (base32 - "11q21p3ki4bn4hb3aix0g775l45l66jmas6m94nfhqqnpjhv4d6g")))) + "1i3nvrd3wjigf1rmgxq1p5xxc3p8v02h5gwi62s30rkrsyjjfjxx")))) (properties `((upstream-name . "org.Mm.eg.db"))) (build-system r-build-system) @@ -8134,14 +8263,14 @@ annotations for the genome of the model mouse Mus musculus.") (define-public r-seqlogo (package (name "r-seqlogo") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqLogo" version)) (sha256 (base32 - "16xvqcdknix9vjm8mrixi6nyfsr45jm844jh1x90m8044lwrsic1")))) + "022vr9ydwcivs7rw7kwj73gfk5gc7ckwa1q66vhd4kw9ylh70v68")))) (properties `((upstream-name . "seqLogo"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/seqLogo") @@ -8249,7 +8378,7 @@ in Biostrings objects.") (define-public r-txdb-mmusculus-ucsc-mm10-knowngene (package (name "r-txdb-mmusculus-ucsc-mm10-knowngene") - (version "3.4.0") + (version "3.4.4") (source (origin (method url-fetch) ;; We cannot use bioconductor-uri here because this tarball is @@ -8260,7 +8389,7 @@ in Biostrings objects.") version ".tar.gz")) (sha256 (base32 - "08gava9wsvpcqz51k2sni3pj03n5155v32d9riqbf305nbirqbkb")))) + "01lgxc1fx5nhlpbwjd5zqghkkbmh6axd98ikx4b0spv0jdg6gf39")))) (properties `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene"))) (build-system r-build-system) @@ -8380,14 +8509,14 @@ Biostrings objects.") (define-public r-motifrg (package (name "r-motifrg") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifRG" version)) (sha256 (base32 - "0mxhyidkyd2zqahdbg69y20r550z78lvr1r3pbjymnwfg4hcfq1p")))) + "1wxww6i0jgyapqclcwy0zzf9kqjvrvylr89z7yhg1izi7jnw2fka")))) (properties `((upstream-name . "motifRG"))) (build-system r-build-system) (propagated-inputs @@ -8432,13 +8561,13 @@ two-dimensional genome scans.") (define-public r-zlibbioc (package (name "r-zlibbioc") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zlibbioc" version)) (sha256 (base32 - "1rwr0mci8a712q0isavi4jmhm94gwivc4nr8j7r4kw05flp4g7gz")))) + "0bjvzy24kab7ank02cc1qk2ikcz4dllgf66wpsdl0d3zp4gn3l2h")))) (properties `((upstream-name . "zlibbioc"))) (build-system r-build-system) @@ -8474,14 +8603,14 @@ secondary structure and comparative analysis in R.") (define-public r-rhtslib (package (name "r-rhtslib") - (version "1.12.1") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhtslib" version)) (sha256 (base32 - "16ywnb8cmr2xabd1i21b92rfziw7xfbv25yv16ipw617p41wa39z")))) + "1h4q54f8za3aaxgy186zf2165sar5c3cgxkk44lq5hzx5pxkl5wn")))) (properties `((upstream-name . "Rhtslib"))) (build-system r-build-system) (propagated-inputs @@ -8501,14 +8630,14 @@ of other R packages who wish to make use of HTSlib.") (define-public r-bamsignals (package (name "r-bamsignals") - (version "1.12.1") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bamsignals" version)) (sha256 (base32 - "141q3p4lzwiqk1mfxi8q1q84axjl0gyiqg59xd3sp4viny4jqmgv")))) + "19irfx1y1izf903vq59wxsdbf88g143zy9l89gxqawh7jfxds8w8")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) @@ -8531,41 +8660,33 @@ paired-end data.") (define-public r-rcas (package (name "r-rcas") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RCAS" version)) (sha256 (base32 - "0vmn7a0rm2ban0kaxrf5danhss2r4hfhnwh5889fjcgqy300fdd5")))) + "0ss5hcg2m7gjji6dd23zxa5bd5a7knwcnada4qs5q2l4clgk39ad")))) (build-system r-build-system) - (native-inputs - `(("r-testthat" ,r-testthat) - ;; During vignette building knitr checks that "pandoc-citeproc" - ;; is in the PATH. - ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1))) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) + `(("r-annotationdbi" ,r-annotationdbi) + ("r-biocgenerics" ,r-biocgenerics) ("r-biomart" ,r-biomart) ("r-biostrings" ,r-biostrings) ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) - ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9) - ("r-bsgenome-celegans-ucsc-ce10" ,r-bsgenome-celegans-ucsc-ce10) - ("r-bsgenome-dmelanogaster-ucsc-dm3" ,r-bsgenome-dmelanogaster-ucsc-dm3) ("r-cowplot" ,r-cowplot) ("r-data-table" ,r-data-table) ("r-dbi" ,r-dbi) ("r-dt" ,r-dt) ("r-genomation" ,r-genomation) + ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) ("r-ggplot2" ,r-ggplot2) ("r-ggseqlogo" ,r-ggseqlogo) ("r-knitr" ,r-knitr) ("r-motifrg" ,r-motifrg) ("r-org-hs-eg-db" ,r-org-hs-eg-db) - ("r-org-ce-eg-db" ,r-org-ce-eg-db) - ("r-org-dm-eg-db" ,r-org-dm-eg-db) - ("r-org-mm-eg-db" ,r-org-mm-eg-db) ("r-pbapply" ,r-pbapply) ("r-pheatmap" ,r-pheatmap) ("r-plotly" ,r-plotly) @@ -8631,14 +8752,14 @@ library implementing most of the pipeline's features.") (define-public r-mutationalpatterns (package (name "r-mutationalpatterns") - (version "1.6.1") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MutationalPatterns" version)) (sha256 (base32 - "1yq7351j42mjxn8fd3c5bdxzb2l5s4lvqhjdvv4rwj4f600n6wj9")))) + "0w9lg1zs106h6rqvy8mhikq6q6q9syw6c1prcxr38ssh85rcih12")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) @@ -8669,14 +8790,14 @@ in SNV base substitution data.") (define-public r-wgcna (package (name "r-wgcna") - (version "1.63") + (version "1.66") (source (origin (method url-fetch) (uri (cran-uri "WGCNA" version)) (sha256 (base32 - "1225dqm68bynkmklnsxdqdd3zqrpzbvqwyly8ibxmk75z33xz309")))) + "0rhnyhzfn93yp24jz9v6dzrmyizwzdw070a7idm0k33w1cm8sjqv")))) (properties `((upstream-name . "WGCNA"))) (build-system r-build-system) (propagated-inputs @@ -8747,13 +8868,14 @@ Sequences.") (version "1.1.4") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/ManuSetty/SeqGL/" - "archive/" version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/ManuSetty/SeqGL.git") + (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 - "0pnk1p3sci5yipyc8xnb6jbmydpl80fld927xgnbcv104hy8h8yh")))) + "1r6ywvhxl3ffv48lgj7sbd582mcc6dha3ksgc2qjlvjrnkbj3799")))) (build-system r-build-system) (propagated-inputs `(("r-biostrings" ,r-biostrings) @@ -8807,13 +8929,13 @@ kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.") (define-public r-tximport (package (name "r-tximport") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tximport" version)) (sha256 (base32 - "1qjc7ah9dzccpvcjrp9k4qnaz13x6kvy1c1xpdj503km6k528lip")))) + "0za2js8hqjgz8ria09cglynffj4w9vrzg85nmn1xgpvmc1xk813h")))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/tximport") (synopsis "Import and summarize transcript-level estimates for gene-level analysis") @@ -8829,13 +8951,13 @@ of gene-level counts.") (define-public r-rhdf5 (package (name "r-rhdf5") - (version "2.24.0") + (version "2.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rhdf5" version)) (sha256 (base32 - "15cmmchhk8bnp94gxg0zk9qyzdjx5kv16dzpbnb62mkq7ydmifx6")))) + "0xmpkfdsmgl79ffffj7cf9fx3zxki2rk0xn25k778kr3s0sbmhis")))) (build-system r-build-system) (propagated-inputs `(("r-rhdf5lib" ,r-rhdf5lib))) @@ -8856,13 +8978,13 @@ the available RAM.") (define-public r-annotationfilter (package (name "r-annotationfilter") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationFilter" version)) (sha256 (base32 - "1w8ypfdz4g7vnwfrvnhjcpm8waciqyq2cn883ajdwg4vv7a5mj9a")))) + "0wrr10cxjzmxx46vjzq2nsf6xlqz1sqwx4xm0sk3d77ff8wmph4x")))) (properties `((upstream-name . "AnnotationFilter"))) (build-system r-build-system) @@ -8915,7 +9037,7 @@ AM_CONDITIONAL(AMPNG, true)")) (("\\$\\(bindir\\)/embossupdate") "")) #t)) (add-after 'disable-update-check 'autogen - (lambda _ (zero? (system* "autoreconf" "-vif"))))))) + (lambda _ (invoke "autoreconf" "-vif") #t))))) (inputs `(("perl" ,perl) ("libpng" ,libpng) @@ -9088,12 +9210,14 @@ group or two ChIP groups run under different conditions.") (name "filevercmp") (version (string-append "0-1." (string-take commit 7))) (source (origin - (method url-fetch) - (uri (string-append "https://github.com/ekg/filevercmp/archive/" - commit ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) - (sha256 - (base32 "0yp5jswf5j2pqc6517x277s4s6h1ss99v57kxw9gy0jkfl3yh450")))) + (method git-fetch) + (uri (git-reference + (url "https://github.com/ekg/filevercmp.git") + (commit commit))) + (file-name (git-file-name name commit)) + (sha256 + (base32 + "1j9vxsy0y050v59h0q1d6501fcw1kjvj0d18l1xk2zyg0jzj247c")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; There are no tests to run. @@ -9103,7 +9227,8 @@ group or two ChIP groups run under different conditions.") (replace 'install (lambda* (#:key outputs #:allow-other-keys) (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) - (install-file "filevercmp" bin))))))) + (install-file "filevercmp" bin) + #t)))))) (home-page "https://github.com/ekg/filevercmp") (synopsis "This program compares version strings") (description "This program compares version strings. It intends to be a @@ -9159,14 +9284,14 @@ common bioinformatics tools.") (define-public r-chipseq (package (name "r-chipseq") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "chipseq" version)) (sha256 (base32 - "09f8dgl5ni75qkf7nvvppwr3irpplv4xb3ks59ld7l8i2mplcrx7")))) + "1pp1rm5fs3hlar5x4dl3a3b4gara7qwf81dbvka6r1n78hrf9x1b")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) @@ -9211,14 +9336,14 @@ GenomicRanges Bioconductor package.") (define-public r-copywriter (package (name "r-copywriter") - (version "2.12.0") + (version "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CopywriteR" version)) (sha256 (base32 - "0b7xwq1va2zclb54f07c5ipmmq4iv2hrlph3j93jz5hmyayv50z3")))) + "0aamxafdk98n7s92jyqs65d6ljpnc2463vanvsw80p44qn6l6awn")))) (properties `((upstream-name . "CopywriteR"))) (build-system r-build-system) (propagated-inputs @@ -9251,13 +9376,13 @@ number detection tools.") (define-public r-methylkit (package (name "r-methylkit") - (version "1.6.1") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "methylKit" version)) (sha256 (base32 - "1hr2czi5ybdf7hdmqsv39d17f3mvmw94wa38bc14zzm9mgy9gfy7")))) + "0mz6lil1wax931incnw5byx0v9i8ryhwq9mv0nv8s48ai33ch3x6")))) (properties `((upstream-name . "methylKit"))) (build-system r-build-system) (propagated-inputs @@ -9297,14 +9422,14 @@ TAB-Seq.") (define-public r-sva (package (name "r-sva") - (version "3.28.0") + (version "3.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "sva" version)) (sha256 (base32 - "0a3jqbz0jp1jxrnjkqfpmca840yqcdwxprdl608bzzx2zb4jl52s")))) + "1xf0hlrqjxl0y3x13mrkxghiv39fd9v2g8gq3qzbf1wj7il6bph3")))) (build-system r-build-system) (propagated-inputs `(("r-genefilter" ,r-genefilter) @@ -9327,14 +9452,14 @@ unmodeled, or latent sources of noise.") (define-public r-seqminer (package (name "r-seqminer") - (version "6.0") + (version "6.1") (source (origin (method url-fetch) (uri (cran-uri "seqminer" version)) (sha256 (base32 - "057j1l6dip35l1aivilapl2zv9db677b3di2pb3sfgq2sxg0ps3l")))) + "15yhg4vfc7jg1jnqb3371j00pgbmbyc9l1xx63hq1l3p34lazq2l")))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) @@ -9381,14 +9506,14 @@ trait.") (define-public r-maldiquant (package (name "r-maldiquant") - (version "1.17") + (version "1.18") (source (origin (method url-fetch) (uri (cran-uri "MALDIquant" version)) (sha256 (base32 - "047s6007ydc38x8wm027mlb4mngz15n0d4238fr8h43wyll5zy0z")))) + "18nl214xjsxkcpbg79jkmw0yznwm5szyh2qb84n7ip46mm779ha6")))) (properties `((upstream-name . "MALDIquant"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/MALDIquant") @@ -9407,14 +9532,14 @@ as allowing spectra with different resolutions.") (define-public r-protgenerics (package (name "r-protgenerics") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ProtGenerics" version)) (sha256 (base32 - "05jbadw2aiwy8vi2ia0jxg06cmwhly2cq4dy1ag7kdxf1c5i9ccn")))) + "053mmxhzncqgigl2iqjlq56qzimlw2zzw31wpzw19rf7rld1vi3b")))) (properties `((upstream-name . "ProtGenerics"))) (build-system r-build-system) (home-page "https://github.com/lgatto/ProtGenerics") @@ -9427,14 +9552,14 @@ proteomics packages.") (define-public r-mzr (package (name "r-mzr") - (version "2.14.0") + (version "2.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mzR" version)) (sha256 (base32 - "190m2bq5bqxhljaj4f7vz9wj5h5laaxd8zp5jampnql6xc4zmarg")) + "0li1y6p95ljiva4lvfmql9sipn4dq42sknbh60b36ycjppnf8lj5")) (modules '((guix build utils))) (snippet '(begin @@ -9456,11 +9581,11 @@ proteomics packages.") #t))))) (inputs `(("boost" ,boost) ; use this instead of the bundled boost sources - ("netcdf" ,netcdf) ("zlib" ,zlib))) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) + ("r-ncdf4" ,r-ncdf4) ("r-protgenerics" ,r-protgenerics) ("r-rcpp" ,r-rcpp) ("r-rhdf5lib" ,r-rhdf5lib) @@ -9479,14 +9604,14 @@ previously been used in XCMS.") (define-public r-affyio (package (name "r-affyio") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affyio" version)) (sha256 (base32 - "0sh5wnnchyfpq5n6rchbqmb27byn7kdzn5rgran6i39c81i5z22n")))) + "1s4zp1211vf0krxzch9v3q3r6vs8hihqppq18i2fpvwlknfja7c1")))) (build-system r-build-system) (propagated-inputs `(("r-zlibbioc" ,r-zlibbioc))) @@ -9503,20 +9628,20 @@ CDF file formats.") (define-public r-affy (package (name "r-affy") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affy" version)) (sha256 (base32 - "0sxq875sigm21sf3qncrfrwfdz9nqw1vldxn3d3hj6aq64jg1ki6")))) + "0x8h4fk2igv7vykqfvf6v9whmx3344v5rf3gyfajd431xkjldz6k")))) (build-system r-build-system) (propagated-inputs `(("r-affyio" ,r-affyio) ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) - ("r-biocinstaller" ,r-biocinstaller) + ("r-biocmanager" ,r-biocmanager) ("r-preprocesscore" ,r-preprocesscore) ("r-zlibbioc" ,r-zlibbioc))) (inputs @@ -9531,14 +9656,14 @@ analysis.") (define-public r-vsn (package (name "r-vsn") - (version "3.48.1") + (version "3.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "vsn" version)) (sha256 (base32 - "0k6mah3g3zqbfap31xmvig4fn452a18xwwa5y0mfj5mj8588p57h")))) + "1g6qkpykw99jm2wv2i61dg2ffwk0n8fm4s5pm2q4c024vw5c9b69")))) (build-system r-build-system) (propagated-inputs `(("r-affy" ,r-affy) @@ -9565,14 +9690,14 @@ and specific in detecting differential transcription.") (define-public r-mzid (package (name "r-mzid") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mzID" version)) (sha256 (base32 - "060k0xlhg8q802c6zsb4b8ps0ccd9ybyaz0gnsvqkxb786i2vk40")))) + "08jbq223viwknsmsi30hyxyxslvmb0l4wx3vmqlkl6qk4vfmxzjz")))) (properties `((upstream-name . "mzID"))) (build-system r-build-system) (propagated-inputs @@ -9595,14 +9720,14 @@ specific parser.") (define-public r-pcamethods (package (name "r-pcamethods") - (version "1.72.0") + (version "1.74.0") (source (origin (method url-fetch) (uri (bioconductor-uri "pcaMethods" version)) (sha256 (base32 - "0v99yf8m7ryh6z0r3z0ggpqfnflcq5bn1q1i1cl9b7q4p6b4sa07")))) + "0ik82s9bsdj4a1mmv0a3k6yisa92mxx7maf3dvip1r8gqlm3dyng")))) (properties `((upstream-name . "pcaMethods"))) (build-system r-build-system) (propagated-inputs @@ -9625,14 +9750,14 @@ structure (pcaRes) to provide a common interface to the PCA results.") (define-public r-msnbase (package (name "r-msnbase") - (version "2.6.1") + (version "2.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnbase" version)) (sha256 (base32 - "0zrpx9r93q5ca2zdak5rs2m9sjm0wjdra1xfj3d3sx6p5gzfyg6n")))) + "0y658anh06vnvbkfs7r8q40gqgyqr2r8kj7jlpnp33fy1lvp1nv7")))) (properties `((upstream-name . "MSnbase"))) (build-system r-build-system) (propagated-inputs @@ -9668,14 +9793,14 @@ of mass spectrometry based proteomics data.") (define-public r-msnid (package (name "r-msnid") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnID" version)) (sha256 (base32 - "172q5chi44104iz4y0g42wrimfp7hlhrfa8vzybx6m0ccrkkhl17")))) + "0hgq4argllhh5hvxqi8vkf1blc3nibsslhx4zsv2mcv4yj75bv4n")))) (properties `((upstream-name . "MSnID"))) (build-system r-build-system) (propagated-inputs @@ -9707,58 +9832,31 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.") (define-public r-seurat (package (name "r-seurat") - (version "2.3.2") + (version "2.3.4") (source (origin (method url-fetch) (uri (cran-uri "Seurat" version)) (sha256 (base32 - "1sjpy5rrpvlpm6hs7qy7qpglgbp7zrgfybcsalpmjb51rhxhgcg1")) - ;; Delete pre-built jar. - (snippet - '(begin (delete-file "inst/java/ModularityOptimizer.jar") - #t)))) + "0l8bv4i9nzz26mirnva10mq6pimibj24vk7vpvfypgn7xk4942hd")))) (properties `((upstream-name . "Seurat"))) (build-system r-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'build-jar - (lambda* (#:key inputs #:allow-other-keys) - (let ((classesdir "tmp-classes")) - (setenv "JAVA_HOME" (assoc-ref inputs "jdk")) - (mkdir classesdir) - (with-output-to-file "manifest" - (lambda _ - (display "Manifest-Version: 1.0 -Main-Class: ModularityOptimizer\n"))) - (and (zero? (apply system* `("javac" "-d" ,classesdir - ,@(find-files "java" "\\.java$")))) - (zero? (system* "jar" - "-cmf" "manifest" - "inst/java/ModularityOptimizer.jar" - "-C" classesdir "."))))))))) - (native-inputs - `(("jdk" ,icedtea "jdk"))) (propagated-inputs `(("r-ape" ,r-ape) - ("r-caret" ,r-caret) ("r-cluster" ,r-cluster) ("r-cowplot" ,r-cowplot) - ("r-diffusionmap" ,r-diffusionmap) ("r-dosnow" ,r-dosnow) ("r-dplyr" ,r-dplyr) ("r-dtw" ,r-dtw) ("r-fitdistrplus" ,r-fitdistrplus) - ("r-fnn" ,r-fnn) ("r-foreach" ,r-foreach) ("r-fpc" ,r-fpc) - ("r-gdata" ,r-gdata) ("r-ggplot2" ,r-ggplot2) ("r-ggridges" ,r-ggridges) ("r-gplots" ,r-gplots) ("r-hdf5r" ,r-hdf5r) ("r-hmisc" ,r-hmisc) + ("r-httr" ,r-httr) ("r-ica" ,r-ica) ("r-igraph" ,r-igraph) ("r-irlba" ,r-irlba) @@ -9771,7 +9869,6 @@ Main-Class: ModularityOptimizer\n"))) ("r-pbapply" ,r-pbapply) ("r-plotly" ,r-plotly) ("r-png" ,r-png) - ("r-ranger" ,r-ranger) ("r-rann" ,r-rann) ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-rcpp" ,r-rcpp) @@ -9782,11 +9879,8 @@ Main-Class: ModularityOptimizer\n"))) ("r-rocr" ,r-rocr) ("r-rtsne" ,r-rtsne) ("r-sdmtools" ,r-sdmtools) - ("r-stringr" ,r-stringr) - ("r-tclust" ,r-tclust) ("r-tidyr" ,r-tidyr) - ("r-tsne" ,r-tsne) - ("r-vgam" ,r-vgam))) + ("r-tsne" ,r-tsne))) (home-page "http://www.satijalab.org/seurat") (synopsis "Seurat is an R toolkit for single cell genomics") (description @@ -9801,14 +9895,14 @@ discovery of differentially expressed genes and markers.") (define-public r-aroma-light (package (name "r-aroma-light") - (version "3.10.0") + (version "3.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "aroma.light" version)) (sha256 (base32 - "1dxsiwsrwcq9mj573f9vpdzrhagdqzal328ma8076px4gg6khxkn")))) + "0vfifgpqxjjncbiv6gvlk9jmj14j90r9f30bqk3ks9v1csjnjhrb")))) (properties `((upstream-name . "aroma.light"))) (build-system r-build-system) (propagated-inputs @@ -9828,14 +9922,14 @@ classes.") (define-public r-deseq (package (name "r-deseq") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DESeq" version)) (sha256 (base32 - "0ykxw8ksif026xy25wx50j2sdsrp156aqkmhcgfjkpgcw699glnm")))) + "1klv1xrh3173srywr6dnq6i7m9djn4gc9aflr1p3a6yjlqcq6fya")))) (properties `((upstream-name . "DESeq"))) (build-system r-build-system) (propagated-inputs @@ -9859,14 +9953,14 @@ distribution.") (define-public r-edaseq (package (name "r-edaseq") - (version "2.14.0") + (version "2.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EDASeq" version)) (sha256 (base32 - "1832pb3jkim4vrqzb8lajwx9r482bhww5n9nz3s6crvyamlp2dj0")))) + "1gjqzn1kg9qwyz2gwjyy9xzzr1lnc7xd5zwdyvzkadz97gckzxwf")))) (properties `((upstream-name . "EDASeq"))) (build-system r-build-system) (propagated-inputs @@ -9897,14 +9991,14 @@ global-scaling and full-quantile normalization.") (define-public r-interactivedisplaybase (package (name "r-interactivedisplaybase") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "interactiveDisplayBase" version)) (sha256 (base32 - "05w58z3i9vkma4jd6rhjaxls4yiq4kwrppgcdq9xrr1pxp99k575")))) + "04xz3dkwan2s5ic1mwkdfnggm0l41mgqfagx160bcsrpkw6z7ark")))) (properties `((upstream-name . "interactiveDisplayBase"))) (build-system r-build-system) @@ -9921,20 +10015,20 @@ Shiny-based display methods for Bioconductor objects.") (define-public r-annotationhub (package (name "r-annotationhub") - (version "2.12.0") + (version "2.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationHub" version)) (sha256 (base32 - "11gh7qkgazs90czdqgv74gh2hz26xrmdp6wsz9x5pygbxls8xdw3")))) + "00288x3na0izpmbcvsqac1br1qwry86vwc2slj1l47crdfb7za6c")))) (properties `((upstream-name . "AnnotationHub"))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) ("r-biocgenerics" ,r-biocgenerics) - ("r-biocinstaller" ,r-biocinstaller) + ("r-biocmanager" ,r-biocmanager) ("r-curl" ,r-curl) ("r-httr" ,r-httr) ("r-interactivedisplaybase" ,r-interactivedisplaybase) @@ -9956,14 +10050,14 @@ by the user, helping with quick and reproducible access.") (define-public r-fastseg (package (name "r-fastseg") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fastseg" version)) (sha256 (base32 - "1yw6hai6hb8qy7akdm4frfp6h4zy93zb68kdj094sanm7kgqmgik")))) + "1l8mdjpfpgwqdss2ywjkb8b4h55wf8v6kmyxdlvy04ds2hj16sb1")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -9986,14 +10080,14 @@ microarrays or GRanges for sequencing data.") (define-public r-keggrest (package (name "r-keggrest") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "KEGGREST" version)) (sha256 (base32 - "1349vidgl9m10l1rbrp3pkwwgi2xcbsw9h9z2xqbvg97lmqc4r8j")))) + "0blpd5a7whd2sswfhqd17h58hg06ymaf80gapdr9ja43hnnlj309")))) (properties `((upstream-name . "KEGGREST"))) (build-system r-build-system) (propagated-inputs @@ -10010,14 +10104,14 @@ microarrays or GRanges for sequencing data.") (define-public r-gage (package (name "r-gage") - (version "2.30.0") + (version "2.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gage" version)) (sha256 (base32 - "0j3cqxy97lpf146wkmdfaq9680gicmzxvhp6w5pxq3j7ipiy7262")))) + "07b098wvryxf0zd423nk6h52s3gyngwjcx2vplqybpbpgl8h2931")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -10039,14 +10133,14 @@ analysis using other methods.") (define-public r-genomicfiles (package (name "r-genomicfiles") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFiles" version)) (sha256 (base32 - "0bhsq5czigrjyl9gkb2kpkpl367b3ac5g8s280adkcxggn9g7sxq")))) + "0qf2yj4lfnnk64fk125n8sqms01shfqiik04nasx2z3k129ykpxp")))) (properties `((upstream-name . "GenomicFiles"))) (build-system r-build-system) (propagated-inputs @@ -10072,14 +10166,14 @@ provide added flexibility for data combination and manipulation.") (define-public r-complexheatmap (package (name "r-complexheatmap") - (version "1.18.1") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ComplexHeatmap" version)) (sha256 (base32 - "0qjwz1hzpjnc90jiinjkikfnr0shi72q3zfdjjz7pxydy0mglq8n")))) + "0s01dzcfj1lmpqfpsbqw7r4858krfzy499lz4cwx4fq3mbyvy2aj")))) (properties `((upstream-name . "ComplexHeatmap"))) (build-system r-build-system) @@ -10102,14 +10196,14 @@ self-defined annotation graphics.") (define-public r-dirichletmultinomial (package (name "r-dirichletmultinomial") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DirichletMultinomial" version)) (sha256 (base32 - "0vcyp81b90in4ls5nbadc66cw2g9aydr94aqifq5j4b7diq74yfs")))) + "19bzn0a5jal1xv0ad6wikxc7wrk582hczqamlln0vb2ffwkj1z3f")))) (properties `((upstream-name . "DirichletMultinomial"))) (build-system r-build-system) @@ -10131,14 +10225,14 @@ originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): (define-public r-ensembldb (package (name "r-ensembldb") - (version "2.4.1") + (version "2.6.2") (source (origin (method url-fetch) (uri (bioconductor-uri "ensembldb" version)) (sha256 (base32 - "1l2b4cxiycv05mz4z4f3dhx57r9ksha02psc114h30ldm5rxz8w6")))) + "0hdz1f34v7sas2v4225icwl3wd4sf17ykpd5dkbx1hc7wcy4w3np")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -10174,21 +10268,21 @@ chromosome region or transcript models of lincRNA genes.") (define-public r-organismdbi (package (name "r-organismdbi") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "OrganismDbi" version)) (sha256 (base32 - "0hb9ni41bjfy5s5ryw2qmqs2sx3i7j47w1g0l8g1pvn7ppnxb6cv")))) + "11pyv56cy4iy095h40k6k0mpjdlh6gsb4ld3s57nfa9nd4ypx3yi")))) (properties `((upstream-name . "OrganismDbi"))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) - ("r-biocinstaller" ,r-biocinstaller) + ("r-biocmanager" ,r-biocmanager) ("r-dbi" ,r-dbi) ("r-genomicfeatures" ,r-genomicfeatures) ("r-genomicranges" ,r-genomicranges) @@ -10206,14 +10300,14 @@ the fact that each of these packages implements a select methods.") (define-public r-biovizbase (package (name "r-biovizbase") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biovizBase" version)) (sha256 (base32 - "0lkiqdr3ics6hgv47lwkykcy761823bbkhffbn4ykyfzyqwl4p67")))) + "0v54mcn3rnnfx8dmcrms5z3rgq19n3hp4r23azlgzwq6hjw7cccx")))) (properties `((upstream-name . "biovizBase"))) (build-system r-build-system) (propagated-inputs @@ -10230,6 +10324,7 @@ the fact that each of these packages implements a select methods.") ("r-hmisc" ,r-hmisc) ("r-iranges" ,r-iranges) ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rlang" ,r-rlang) ("r-rsamtools" ,r-rsamtools) ("r-s4vectors" ,r-s4vectors) ("r-scales" ,r-scales) @@ -10247,14 +10342,14 @@ effort and encourages consistency.") (define-public r-ggbio (package (name "r-ggbio") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ggbio" version)) (sha256 (base32 - "0wszh3w8yia5zw758h837i1q35k99sn444y2hahcxqbdmmlbf7in")))) + "0wq49qqzkcn8s19xgaxf2s1j1a563d7pbhhvris6fhxfdjsz4934")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -10277,6 +10372,7 @@ effort and encourages consistency.") ("r-iranges" ,r-iranges) ("r-organismdbi" ,r-organismdbi) ("r-reshape2" ,r-reshape2) + ("r-rlang" ,r-rlang) ("r-rsamtools" ,r-rsamtools) ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors) @@ -10299,14 +10395,14 @@ interval to data view, mismatch pileup, and several splicing summaries.") (define-public r-gprofiler (package (name "r-gprofiler") - (version "0.6.6") + (version "0.6.7") (source (origin (method url-fetch) (uri (cran-uri "gProfileR" version)) (sha256 (base32 - "1n6cj12j102b4x9vhyl4dljp1i0r43p23cnhqbx4als2xfxdlqgi")))) + "12nwidbnqmnfy5dnqga26byslvdnkrpz2fi19qfcby6xx0wbndk7")))) (properties `((upstream-name . "gProfileR"))) (build-system r-build-system) (propagated-inputs @@ -10323,14 +10419,14 @@ organisms via the @code{g:Profiler} toolkit.") (define-public r-gqtlbase (package (name "r-gqtlbase") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gQTLBase" version)) (sha256 (base32 - "1m3ajpqjhw1nwwsn372r44xfxq0a9a0pzsnrprzdjp6mh52p9b5m")))) + "1lbk1m1mkvbk30flk5pf3pcrnm2s0sj5r48kbjgad39dsvd8zgqx")))) (properties `((upstream-name . "gQTLBase"))) (build-system r-build-system) (propagated-inputs @@ -10358,14 +10454,14 @@ and more.") (define-public r-snpstats (package (name "r-snpstats") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "snpStats" version)) (sha256 (base32 - "0iydgfnm053iw860qa1bbh4f6nwzlsf3vhgq92gvl2v4xsz1jbbs")))) + "1pplx4pf9bqi7v5v1l74yknc1s61carvbqkf327ky7vbvp0bck33")))) (properties `((upstream-name . "snpStats"))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) @@ -10417,14 +10513,14 @@ several related annotation packages.") (define-public r-erma (package (name "r-erma") - (version "0.12.0") + (version "0.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "erma" version)) (sha256 (base32 - "1ka68n18yizlyvb8bpwwcl4hqbsasg8hw8jb3vgy3cd4szji87hh")))) + "0hj9iz904rr1y66442lkxjywkw1ydyxxlhmjirawbf09ic5ad4g9")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -10455,14 +10551,14 @@ by Ernst and Kellis.") (define-public r-ldblock (package (name "r-ldblock") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ldblock" version)) (sha256 (base32 - "0c24zvnwsp39d3q0bps13sc441jj9ms2zi34xsb8c392lqmbypvd")))) + "0xbf4pmhrk5fnd1iz5wzjvdr75v114bwpznhcig4wiqmxc27sips")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) @@ -10487,14 +10583,14 @@ defining LD blocks.") (define-public r-gqtlstats (package (name "r-gqtlstats") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gQTLstats" version)) (sha256 (base32 - "19g8qhfgngdc14cw9k4i44cxhs3qva87x56gjzmn25k1yj8qgsp1")))) + "1sg9kw59dlayj7qxql9pd93d4hmml504sa3kkfpzfh3xri7m5pxf")))) (properties `((upstream-name . "gQTLstats"))) (build-system r-build-system) (propagated-inputs @@ -10541,14 +10637,14 @@ family of feature/genome hypotheses.") (define-public r-gviz (package (name "r-gviz") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Gviz" version)) (sha256 (base32 - "1fhli7ahkl5r43j0hc89ib41mfadj6qyrg36i03ncz8zs6iqwpx4")))) + "05zk9hf30afg6rjg97lzn5v8xij90v8zm09y9vcz0asmc3c8xs0a")))) (properties `((upstream-name . "Gviz"))) (build-system r-build-system) (propagated-inputs @@ -10587,14 +10683,14 @@ with your data.") (define-public r-gwascat (package (name "r-gwascat") - (version "2.12.0") + (version "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gwascat" version)) (sha256 (base32 - "08ba9il4vbjjwlbwmqg4ai6ya1p09js9agn95sw0dhc9gqln42hx")))) + "1fnyjydhicq4ayrv0lqjv48h9bd72h40s6l82g1h2ng0icwz38g0")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -10627,13 +10723,13 @@ EMBL-EBI GWAS catalog.") (define-public r-sushi (package (name "r-sushi") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Sushi" version)) (sha256 (base32 - "1m15hmg4k0qhshyn65xfj5hx7xbaf0kxqw70lxisak6pj1w00l41")))) + "0dv5di0hgbvk9cxnqhyf18mdjl50k6bk00a89r6zgp83rbxwr1r8")))) (properties `((upstream-name . "Sushi"))) (build-system r-build-system) (propagated-inputs @@ -10649,13 +10745,13 @@ visualizations for publication-quality multi-panel figures.") (define-public r-fithic (package (name "r-fithic") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "FitHiC" version)) (sha256 (base32 - "06w4q836bi1mvkbl1saghv4r5p4hxpjg8cp7kgad13ls450kqmyd")))) + "15xd8mz7660q4zr9p74mq1pqps4iz7pxp8f9ifn21gwg94aq1avn")))) (properties `((upstream-name . "FitHiC"))) (build-system r-build-system) (propagated-inputs @@ -10673,13 +10769,13 @@ assays such as Hi-C.") (define-public r-hitc (package (name "r-hitc") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HiTC" version)) (sha256 (base32 - "0qkk5139f51lwwy1yh7nbkflh5d69prirmhniwam34nlg9rzjm2z")))) + "11f96k1707g6milpjgnrjf3b5r42hsrxhb5d8znkcr3y3mrskdbj")))) (properties `((upstream-name . "HiTC"))) (build-system r-build-system) (propagated-inputs @@ -10702,14 +10798,14 @@ provided.") (define-public r-qvalue (package (name "r-qvalue") - (version "2.12.0") + (version "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "qvalue" version)) (sha256 (base32 - "1ndwkj0hh7v4lwylq1v0fkxqs7mfmbcj8kxbdpj1wkvf131z2ns8")))) + "03qxshqwwq1rj23p6pjrz08jm3ziikvy9badi4mz2rcwy2nz783a")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) @@ -10731,14 +10827,14 @@ problems in genomics, brain imaging, astrophysics, and data mining.") (define-public r-hdf5array (package (name "r-hdf5array") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HDF5Array" version)) (sha256 (base32 - "1l0276qxkhgdxsfck3jmi8jvnsr20g10gjki53g0mqa45wnhm3ck")))) + "1w7ad8cfsbh5xx82m3l4lc0vbmj9lcsqxxpiy3ana2ycgn1bqv3g")))) (properties `((upstream-name . "HDF5Array"))) (build-system r-build-system) (propagated-inputs @@ -10757,14 +10853,20 @@ block processing.") (define-public r-rhdf5lib (package (name "r-rhdf5lib") - (version "1.2.1") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhdf5lib" version)) (sha256 (base32 - "1y59acac6v8hrhv84gghn9ifsni9xxxacaj177rrl4frmkrz4x3c")))) + "01gpz780g850ql20b2ql6pvr678ydk4nq4sn5iiih94a4crb9lz1")) + (modules '((guix build utils))) + (snippet + '(begin + ;; Delete bundled binaries + (delete-file-recursively "src/winlib/") + #t)))) (properties `((upstream-name . "Rhdf5lib"))) (build-system r-build-system) (arguments @@ -10781,7 +10883,7 @@ block processing.") "'%s/libhdf5.a %s/libhdf5.a -lz'")) (with-directory-excursion "src" (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source")) - (rename-file (string-append "hdf5-" ,(package-version hdf5)) + (rename-file (string-append "hdf5-" ,(package-version hdf5-1.10)) "hdf5") ;; Remove timestamp and host system information to make ;; the build reproducible. @@ -10810,9 +10912,9 @@ block processing.") (inputs `(("zlib" ,zlib))) (propagated-inputs - `(("hdf5" ,hdf5))) + `(("hdf5" ,hdf5-1.10))) (native-inputs - `(("hdf5-source" ,(package-source hdf5)))) + `(("hdf5-source" ,(package-source hdf5-1.10)))) (home-page "https://bioconductor.org/packages/Rhdf5lib") (synopsis "HDF5 library as an R package") (description "This package provides C and C++ HDF5 libraries for use in R @@ -10822,20 +10924,21 @@ packages.") (define-public r-beachmat (package (name "r-beachmat") - (version "1.2.1") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "beachmat" version)) (sha256 (base32 - "1w90v0jx1zgrfxzx99gdkk0dz2vi25hr51jml1bvq33i64rj7996")))) + "07zgmms0qg8gw7x0js46965bbhpfj2aa1h5ixdz9r332bxv9cdmr")))) (build-system r-build-system) (inputs `(("hdf5" ,hdf5) ("zlib" ,zlib))) (propagated-inputs - `(("r-delayedarray" ,r-delayedarray) + `(("r-biocgenerics" ,r-biocgenerics) + ("r-delayedarray" ,r-delayedarray) ("r-hdf5array" ,r-hdf5array) ("r-rcpp" ,r-rcpp) ("r-rhdf5" ,r-rhdf5) @@ -10850,14 +10953,14 @@ matrices.") (define-public r-singlecellexperiment (package (name "r-singlecellexperiment") - (version "1.2.0") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SingleCellExperiment" version)) (sha256 (base32 - "0mz3chia250v8v6q8r5cqv5fc4bpcw1hhrfr3p7l5i4xi85scpka")))) + "19r4r7djrn46qlijkj1g926vcklxzcrxjlxv6cg43m9j9jgfs3dj")))) (properties `((upstream-name . "SingleCellExperiment"))) (build-system r-build-system) @@ -10877,39 +10980,31 @@ libraries.") (define-public r-scater (package (name "r-scater") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scater" version)) (sha256 (base32 - "0bhpikgz3b9f510dawsay4zry9rlp8vjx5n6zvwbcpwrd94p3903")))) + "1kwa9n70c5j0xcj6nkmlkzjr63cnj78mp8nhg58n07fq1ijm4ns3")))) (build-system r-build-system) (propagated-inputs `(("r-beachmat" ,r-beachmat) - ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) - ("r-data-table" ,r-data-table) + ("r-biocparallel" ,r-biocparallel) ("r-delayedarray" ,r-delayedarray) ("r-delayedmatrixstats" ,r-delayedmatrixstats) ("r-dplyr" ,r-dplyr) - ("r-edger" ,r-edger) ("r-ggbeeswarm" ,r-ggbeeswarm) ("r-ggplot2" ,r-ggplot2) - ("r-limma" ,r-limma) ("r-matrix" ,r-matrix) ("r-plyr" ,r-plyr) ("r-rcpp" ,r-rcpp) ("r-reshape2" ,r-reshape2) - ("r-rhdf5" ,r-rhdf5) ("r-rhdf5lib" ,r-rhdf5lib) - ("r-rjson" ,r-rjson) ("r-s4vectors" ,r-s4vectors) - ("r-shiny" ,r-shiny) - ("r-shinydashboard" ,r-shinydashboard) ("r-singlecellexperiment" ,r-singlecellexperiment) ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-tximport" ,r-tximport) ("r-viridis" ,r-viridis))) (home-page "https://github.com/davismcc/scater") (synopsis "Single-cell analysis toolkit for gene expression data in R") @@ -10921,26 +11016,24 @@ quality control.") (define-public r-scran (package (name "r-scran") - (version "1.8.2") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "scran" version)) (sha256 (base32 - "0nbn5x75gf9d0p18w7vpkbv30cpdqvp5bz8xvila0h7jla7xdyih")))) + "1viyzrwfm9vccsf54c6g7k1dn7skkfx4ml1jy12q67wa20sx8l03")))) (build-system r-build-system) (propagated-inputs `(("r-beachmat" ,r-beachmat) ("r-biocgenerics" ,r-biocgenerics) + ("r-biocneighbors" ,r-biocneighbors) ("r-biocparallel" ,r-biocparallel) ("r-delayedarray" ,r-delayedarray) ("r-delayedmatrixstats" ,r-delayedmatrixstats) - ("r-dt" ,r-dt) ("r-dynamictreecut" ,r-dynamictreecut) ("r-edger" ,r-edger) - ("r-fnn" ,r-fnn) - ("r-ggplot2" ,r-ggplot2) ("r-igraph" ,r-igraph) ("r-limma" ,r-limma) ("r-matrix" ,r-matrix) @@ -10948,11 +11041,9 @@ quality control.") ("r-rhdf5lib" ,r-rhdf5lib) ("r-s4vectors" ,r-s4vectors) ("r-scater" ,r-scater) - ("r-shiny" ,r-shiny) ("r-singlecellexperiment" ,r-singlecellexperiment) ("r-statmod" ,r-statmod) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-viridis" ,r-viridis))) + ("r-summarizedexperiment" ,r-summarizedexperiment))) (home-page "https://bioconductor.org/packages/scran") (synopsis "Methods for single-cell RNA-Seq data analysis") (description "This package implements a variety of low-level analyses of @@ -10964,19 +11055,21 @@ variable and significantly correlated genes.") (define-public r-delayedmatrixstats (package (name "r-delayedmatrixstats") - (version "1.2.0") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedMatrixStats" version)) (sha256 (base32 - "1dasghfy8x27zzmd0igag4mc1gxxxbchsl4hpc1050dj3wnw9w3y")))) + "03fk2avl1vyjv2wslczkc82qr0zmp1ra8iimd47pbmnnm839ly4w")))) (properties `((upstream-name . "DelayedMatrixStats"))) (build-system r-build-system) (propagated-inputs - `(("r-delayedarray" ,r-delayedarray) + `(("r-biocparallel" ,r-biocparallel) + ("r-delayedarray" ,r-delayedarray) + ("r-hdf5array" ,r-hdf5array) ("r-iranges" ,r-iranges) ("r-matrix" ,r-matrix) ("r-matrixstats" ,r-matrixstats) @@ -11075,7 +11168,7 @@ droplet sequencing. It has been particularly tailored for Drop-seq.") (define-public sambamba (package (name "sambamba") - (version "0.6.7-10-g223fa20") + (version "0.6.8") (source (origin (method git-fetch) @@ -11085,7 +11178,7 @@ droplet sequencing. It has been particularly tailored for Drop-seq.") (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "1zb9hrxglxqh13ava9wwri30cvf85hjnbn8ccnr8l60a3k5avczn")))) + "0k0cz3qcv98p6cq09zlbgnjsggxcqbcmzxg5zikgcgbr2nfq4lry")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; there is no test target @@ -11096,9 +11189,10 @@ droplet sequencing. It has been particularly tailored for Drop-seq.") (add-after 'unpack 'fix-ldc-version (lambda _ (substitute* "gen_ldc_version_info.py" - (("/usr/bin/env.*") (which "python"))) + (("/usr/bin/env.*") (which "python3"))) (substitute* "Makefile" - (("\\$\\(shell which ldmd2\\)") (which "ldmd2"))) + ;; We use ldc2 instead of ldmd2 to compile sambamba. + (("\\$\\(shell which ldmd2\\)") (which "ldc2"))) #t)) (add-after 'unpack 'place-biod-and-undead (lambda* (#:key inputs #:allow-other-keys) @@ -11110,21 +11204,21 @@ droplet sequencing. It has been particularly tailored for Drop-seq.") (substitute* "Makefile" (("htslib/libhts.a lz4/lib/liblz4.a") "-L-lhts -L-llz4") - ((" htslib-static lz4-static") "")) + ((" lz4-static htslib-static") "")) #t)) (replace 'install (lambda* (#:key outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) (bin (string-append out "/bin"))) (mkdir-p bin) - (install-file "build/sambamba" bin) + (install-file "bin/sambamba" bin) #t)))))) (native-inputs `(("ldc" ,ldc) ("rdmd" ,rdmd) - ("python" ,python2-minimal) + ("python" ,python-minimal) ("biod" - ,(let ((commit "c778e4f2d8bacea7499283ce39f5577b232732c6")) + ,(let ((commit "4f1a7d2fb7ef3dfe962aa357d672f354ebfbe42e")) (origin (method git-fetch) (uri (git-reference @@ -11135,20 +11229,20 @@ droplet sequencing. It has been particularly tailored for Drop-seq.") "-checkout")) (sha256 (base32 - "1z90562hg47i63gx042wb3ak2vqjg5z7hwgn9bp2pdxfg3nxrw37"))))) + "1k5pdjv1qvi0a3rwd1sfq6zbj37l86i7bf710m4c0y6737lxj426"))))) ("undead" - ,(let ((commit "92803d25c88657e945511f0976a0c79d8da46e89")) + ,(let ((commit "9be93876982b5f14fcca60832563b3cd767dd84d")) (origin (method git-fetch) (uri (git-reference - (url "https://github.com/dlang/undeaD.git") + (url "https://github.com/biod/undeaD.git") (commit commit))) (file-name (string-append "undead-" (string-take commit 9) "-checkout")) (sha256 (base32 - "0vq6n81vzqvgphjw54lz2isc1j8lcxwjdbrhqz1h5gwrvw9w5138"))))))) + "1xfarj0nqlmi5jd1vmcmm7pabzaf9hxyvk6hp0d6jslb5k9r8r3d"))))))) (inputs `(("lz4" ,lz4) ("htslib" ,htslib-for-sambamba))) @@ -11164,16 +11258,16 @@ sort, markdup, and depth.") (define-public ritornello (package (name "ritornello") - (version "1.0.0") + (version "2.0.1") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/KlugerLab/" - "Ritornello/archive/v" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/KlugerLab/Ritornello.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "02nik86gq9ljjriv6pamwlmqnfky3ads1fpklx6mc3hx6k40pg38")))) + "1xahvq215qld7x1w8vpa5zbrsj6p9crb9shqa2x89sb0aaxa02jk")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; there are no tests @@ -11182,7 +11276,7 @@ sort, markdup, and depth.") (add-after 'unpack 'patch-samtools-references (lambda* (#:key inputs #:allow-other-keys) (substitute* '("src/SamStream.h" - "src/BufferedGenomeReader.h") + "src/FLD.cpp") (("<sam.h>") "<samtools/sam.h>")) #t)) (delete 'configure) @@ -11408,15 +11502,16 @@ applications for tackling some common problems in a user-friendly way.") (define-public tadbit (package (name "tadbit") - (version "0.2") + (version "0.2.0") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/3DGenomes/TADbit/" - "archive/v" version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/3DGenomes/TADbit.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "1cnfqrl4685zar4nnw94j94nhvl2h29jm448nadqi1h05z6fdk4f")))) + "07g3aj648prmsvxp9caz5yl41k0y0647vxh0f5p3w8376mfiljd0")))) (build-system python-build-system) (arguments `(;; Tests are included and must be run after installation, but @@ -11471,13 +11566,14 @@ models. TADbit is complemented by TADkit for visualizing 3D models.") (version "302.0.0") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/ENCODE-DCC/kentUtils/" - "archive/v" version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/ENCODE-DCC/kentUtils.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "134aja3k1cj32kbk1nnw0q9gxjb2krr15q6sga8qldzvc0585rmm")) + "0n1wbyjpzii2b9qhyp9r1q76j623cggpg3y8fmw78ld3z4y7ivha")) (modules '((guix build utils) (srfi srfi-26) (ice-9 ftw))) @@ -11528,6 +11624,8 @@ models. TADbit is complemented by TADkit for visualizing 3D models.") #:tests? #f #:phases (modify-phases %standard-phases + (add-after 'unpack 'fix-permissions + (lambda _ (make-file-writable "src/inc/localEnvironment.mk") #t)) (add-after 'unpack 'fix-paths (lambda _ (substitute* "Makefile" @@ -11772,19 +11870,39 @@ using nucleotide or amino-acid sequence data.") (define-public kallisto (package (name "kallisto") - (version "0.43.1") + (version "0.44.0") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/pachterlab/" - "kallisto/archive/v" version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/pachterlab/kallisto.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "03j3iqhvq7ya3c91gidly3k3jvgm97vjq4scihrlxh315j696r11")))) + "0nj382jiywqnpgvyhichajpkkh5r0bapn43f4dx40zdaq5v4m40m")))) (build-system cmake-build-system) - (arguments `(#:tests? #f)) ; no "check" target + (arguments + `(#:tests? #f ; no "check" target + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'do-not-use-bundled-htslib + (lambda _ + (substitute* "CMakeLists.txt" + (("^ExternalProject_Add" m) + (string-append "if (NEVER)\n" m)) + (("^\\)") + (string-append ")\nendif(NEVER)")) + (("include_directories\\(\\$\\{htslib_PREFIX.*" m) + (string-append "# " m))) + (substitute* "src/CMakeLists.txt" + (("target_link_libraries\\(kallisto kallisto_core pthread \ +\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/../ext/htslib/libhts.a\\)") + "target_link_libraries(kallisto kallisto_core pthread hts)") + (("include_directories\\(\\.\\./ext/htslib\\)") "")) + #t))))) (inputs `(("hdf5" ,hdf5) + ("htslib" ,htslib) ("zlib" ,zlib))) (home-page "http://pachterlab.github.io/kallisto/") (synopsis "Near-optimal RNA-Seq quantification") @@ -11803,14 +11921,14 @@ accurate as existing quantification tools.") (name "libgff") (version "1.0") (source (origin - (method url-fetch) - (uri (string-append - "https://github.com/Kingsford-Group/" - "libgff/archive/v" version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/Kingsford-Group/libgff.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "0vc4nxyhlm6g9vvmx5l4lfs5pnvixsv1hiiy4kddf2y3p6jna8ls")))) + "0n6vfjnq7a2mianipscbshrvbncss8z4zkgkbjw754p9043nfkps")))) (build-system cmake-build-system) (arguments `(#:tests? #f)) ; no tests included (home-page "https://github.com/Kingsford-Group/libgff") @@ -11855,14 +11973,14 @@ bytes of memory space, where n is the length of the string.") (name "sailfish") (version "0.10.1") (source (origin - (method url-fetch) - (uri - (string-append "https://github.com/kingsfordgroup/" - "sailfish/archive/v" version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/kingsfordgroup/sailfish.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "1inn60dxiwsz8g9w7kvfhjxj4bwfb0r12dyhpzzhfbig712dkmm0")) + "1amcc5hqvsl42hg4x19bi9vy47cl874s0lw1fmi0hwsdk9i8c03v")) (modules '((guix build utils))) (snippet '(begin @@ -11899,27 +12017,30 @@ bytes of memory space, where n is the length of the string.") (add-after 'unpack 'do-not-look-for-boost (lambda* (#:key inputs #:allow-other-keys) (substitute* "CMakeLists.txt" - (("find_package\\(Boost 1\\.53\\.0") "#")))) + (("find_package\\(Boost 1\\.53\\.0") "#")) + #t)) (add-after 'unpack 'do-not-assign-to-macro (lambda _ (substitute* "include/spdlog/details/format.cc" - (("const unsigned CHAR_WIDTH = 1;") "")))) + (("const unsigned CHAR_WIDTH = 1;") "")) + #t)) (add-after 'unpack 'prepare-rapmap (lambda* (#:key inputs #:allow-other-keys) (let ((src "external/install/src/rapmap/") (include "external/install/include/rapmap/") (rapmap (assoc-ref inputs "rapmap"))) (mkdir-p "/tmp/rapmap") - (system* "tar" "xf" - (assoc-ref inputs "rapmap") - "-C" "/tmp/rapmap" - "--strip-components=1") + (invoke "tar" "xf" + (assoc-ref inputs "rapmap") + "-C" "/tmp/rapmap" + "--strip-components=1") (mkdir-p src) (mkdir-p include) (for-each (lambda (file) (install-file file src)) (find-files "/tmp/rapmap/src" "\\.(c|cpp)")) - (copy-recursively "/tmp/rapmap/include" include)))) + (copy-recursively "/tmp/rapmap/include" include)) + #t)) (add-after 'unpack 'use-system-libraries (lambda* (#:key inputs #:allow-other-keys) (substitute* '("src/SailfishIndexer.cpp" @@ -11959,7 +12080,8 @@ bytes of memory space, where n is the length of the string.") (string-append (getenv "CPLUS_INCLUDE_PATH") ":" (assoc-ref inputs "eigen") - "/include/eigen3"))))))) + "/include/eigen3")) + #t))))) (inputs `(("boost" ,boost) ("eigen" ,eigen) @@ -12145,11 +12267,13 @@ performance as its primary goal.") (add-after 'unpack 'do-not-look-for-boost (lambda* (#:key inputs #:allow-other-keys) (substitute* "CMakeLists.txt" - (("find_package\\(Boost 1\\.53\\.0") "#")))) + (("find_package\\(Boost 1\\.53\\.0") "#")) + #t)) (add-after 'unpack 'do-not-phone-home (lambda _ (substitute* "src/Salmon.cpp" - (("getVersionMessage\\(\\)") "\"\"")))) + (("getVersionMessage\\(\\)") "\"\"")) + #t)) (add-after 'unpack 'prepare-rapmap (lambda* (#:key inputs #:allow-other-keys) (let ((src "external/install/src/rapmap/") @@ -12166,7 +12290,8 @@ performance as its primary goal.") "external/install/include/rapmap/concurrentqueue.h" "external/install/include/rapmap/FastxParserThreadUtils.hpp" "external/install/src/rapmap/FastxParser.cpp" - "external/install/src/rapmap/xxhash.c"))))) + "external/install/src/rapmap/xxhash.c"))) + #t)) (add-after 'unpack 'use-system-libraries (lambda* (#:key inputs #:allow-other-keys) (substitute* "src/CMakeLists.txt" @@ -12277,8 +12402,7 @@ variational inference.") (propagated-inputs `(("python-h5py" ,python-h5py) ("python-numpy" ,python-numpy) - ("python-scipy" ,python-scipy) - ("python-typing" ,python-typing))) + ("python-scipy" ,python-scipy))) (home-page "https://github.com/linnarsson-lab/loompy") (synopsis "Work with .loom files for single-cell RNA-seq data") (description "The loom file format is an efficient format for very large @@ -12884,8 +13008,8 @@ once. This package provides tools to perform Drop-seq analyses.") ("r-rtracklayer" ,r-rtracklayer) ("r-rjson" ,r-rjson) ("salmon" ,salmon) - ("ghc-pandoc" ,ghc-pandoc-1) - ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1) + ("ghc-pandoc" ,ghc-pandoc) + ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc) ("python-wrapper" ,python-wrapper) ("python-pyyaml" ,python-pyyaml))) (home-page "http://bioinformatics.mdc-berlin.de/pigx/") @@ -12946,12 +13070,12 @@ expression report comparing samples in an easily configurable manner.") ("macs" ,macs) ("multiqc" ,multiqc) ("perl" ,perl) - ("ghc-pandoc" ,ghc-pandoc-1) - ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1) + ("ghc-pandoc" ,ghc-pandoc) + ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc) ("fastqc" ,fastqc) ("bowtie" ,bowtie) ("idr" ,idr) - ("snakemake" ,snakemake-4) + ("snakemake" ,snakemake) ("samtools" ,samtools) ("bedtools" ,bedtools) ("kentutils" ,kentutils))) @@ -13008,11 +13132,11 @@ in an easily configurable manner.") ("r-bookdown" ,r-bookdown) ("r-ggplot2" ,r-ggplot2) ("r-ggbio" ,r-ggbio) - ("ghc-pandoc" ,ghc-pandoc-1) - ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1) + ("ghc-pandoc" ,ghc-pandoc) + ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc) ("python-wrapper" ,python-wrapper) ("python-pyyaml" ,python-pyyaml) - ("snakemake" ,snakemake-4) + ("snakemake" ,snakemake) ("bismark" ,bismark) ("fastqc" ,fastqc) ("bowtie" ,bowtie) @@ -13059,10 +13183,10 @@ methylation and segmentation.") ("python-magic" ,python-magic) ("python-numpy" ,python-numpy) ("python-loompy" ,python-loompy) - ("ghc-pandoc" ,ghc-pandoc-1) - ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1) + ("ghc-pandoc" ,ghc-pandoc) + ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc) ("samtools" ,samtools) - ("snakemake" ,snakemake-4) + ("snakemake" ,snakemake) ("star" ,star) ("r-minimal" ,r-minimal) ("r-argparser" ,r-argparser) @@ -13458,3 +13582,873 @@ conversions, region filtering, FASTA sequence extraction and more.") spliced (back-spliced) sequencing reads, indicative of circular RNA (circRNA) in RNA-seq data.") (license license:gpl3)))) + +(define-public python-scanpy + (package + (name "python-scanpy") + (version "1.2.2") + (source + (origin + (method url-fetch) + (uri (pypi-uri "scanpy" version)) + (sha256 + (base32 + "1ak7bxms5a0yvf65prppq2g38clkv7c7jnjbnfpkh3xxv7q512jz")))) + (build-system python-build-system) + (propagated-inputs + `(("python-anndata" ,python-anndata) + ("python-igraph" ,python-igraph) + ("python-numba" ,python-numba) + ("python-joblib" ,python-joblib) + ("python-natsort" ,python-natsort) + ("python-networkx" ,python-networkx) + ("python-statsmodels" ,python-statsmodels) + ("python-scikit-learn" ,python-scikit-learn) + ("python-matplotlib" ,python-matplotlib) + ("python-pandas" ,python-pandas) + ("python-scipy" ,python-scipy) + ("python-seaborn" ,python-seaborn) + ("python-h5py" ,python-h5py) + ("python-tables" ,python-tables))) + (home-page "http://github.com/theislab/scanpy") + (synopsis "Single-Cell Analysis in Python.") + (description "Scanpy is a scalable toolkit for analyzing single-cell gene +expression data. It includes preprocessing, visualization, clustering, +pseudotime and trajectory inference and differential expression testing. The +Python-based implementation efficiently deals with datasets of more than one +million cells.") + (license license:bsd-3))) + +(define-public gffcompare + (let ((commit "be56ef4349ea3966c12c6397f85e49e047361c41") + (revision "1")) + (package + (name "gffcompare") + (version (git-version "0.10.15" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/gpertea/gffcompare/") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0cp5qpxdhw4mxpya5dld8wi3jk00zyklm6rcri426wydinrnfmkg")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; no check target + #:phases + (modify-phases %standard-phases + (delete 'configure) + (add-before 'build 'copy-gclib-source + (lambda* (#:key inputs #:allow-other-keys) + (mkdir "../gclib") + (copy-recursively + (assoc-ref inputs "gclib-source") "../gclib") + #t)) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) + (install-file "gffcompare" bin) + #t)))))) + (native-inputs + `(("gclib-source" ; see 'README.md' of gffcompare + ,(let ((commit "54917d0849c1e83cfb057b5f712e5cb6a35d948f") + (revision "1") + (name "gclib") + (version (git-version "0.10.3" revision commit))) + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/gpertea/gclib/") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0b51lc0b8syrv7186fd7n8f15rwnf264qgfmm2palrwks1px24mr"))))))) + (home-page "https://github.com/gpertea/gffcompare/") + (synopsis "Tool for comparing or classifing transcripts of RNA-Seq") + (description + "@code{gffcompare} is a tool that can: +@enumerate +@item compare and evaluate the accuracy of RNA-Seq transcript assemblers +(Cufflinks, Stringtie); +@item collapse (merge) duplicate transcripts from multiple GTF/GFF3 files (e.g. +resulted from assembly of different samples); +@item classify transcripts from one or multiple GTF/GFF3 files as they relate to +reference transcripts provided in a annotation file (also in GTF/GFF3 format). +@end enumerate") + (license + (list + license:expat ;license for gffcompare + license:artistic2.0))))) ;license for gclib + +(define-public python-intervaltree + (package + (name "python-intervaltree") + (version "2.1.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "intervaltree" version)) + (sha256 + (base32 + "02w191m9zxkcjqr1kv2slxvhymwhj3jnsyy3a28b837pi15q19dc")))) + (build-system python-build-system) + ;; FIXME: error when collecting tests + (arguments '(#:tests? #f)) + (propagated-inputs + `(("python-sortedcontainers" ,python-sortedcontainers))) + (native-inputs + `(("python-pytest" ,python-pytest))) + (home-page "https://github.com/chaimleib/intervaltree") + (synopsis "Editable interval tree data structure") + (description + "This package provides a mutable, self-balancing interval tree +implementation for Python. Queries may be by point, by range overlap, or by +range envelopment. This library was designed to allow tagging text and time +intervals, where the intervals include the lower bound but not the upper +bound.") + (license license:asl2.0))) + +(define-public python-pypairix + (package + (name "python-pypairix") + (version "0.3.6") + (source + (origin + (method url-fetch) + (uri (pypi-uri "pypairix" version)) + (sha256 + (base32 + "0zs92b74s5v4xy2h16s15f3z6l4nnbw8x8zyif7xx5xpafjn0xss")))) + (build-system python-build-system) + ;; FIXME: the tests fail because test.support cannot be loaded: + ;; ImportError: cannot import name 'support' + (arguments '(#:tests? #f)) + (inputs + `(("zlib" ,zlib))) + (home-page "https://github.com/4dn-dcic/pairix") + (synopsis "Support for querying pairix-indexed bgzipped text files") + (description + "Pypairix is a Python module for fast querying on a pairix-indexed +bgzipped text file that contains a pair of genomic coordinates per line.") + (license license:expat))) + +(define-public python-pyfaidx + (package + (name "python-pyfaidx") + (version "0.5.4.2") + (source + (origin + (method url-fetch) + (uri (pypi-uri "pyfaidx" version)) + (sha256 + (base32 + "0y5zyjksj1rdglj601xd2bbni5abhdh622y3ck76chyzxz9z4rx8")))) + (build-system python-build-system) + (propagated-inputs + `(("python-setuptools" ,python-setuptools) + ("python-six" ,python-six))) + (home-page "http://mattshirley.com") + (synopsis "Random access to fasta subsequences") + (description + "This package provides procedures for efficient pythonic random access to +fasta subsequences.") + (license license:bsd-3))) + +(define-public python-cooler + (package + (name "python-cooler") + (version "0.7.11") + (source + (origin + (method url-fetch) + (uri (pypi-uri "cooler" version)) + (sha256 + (base32 + "08k5nxnxa6qsbk15z5z0q01n28042k87wi4905hh95rzqib15mhx")))) + (build-system python-build-system) + (propagated-inputs + `(("python-biopython" ,python-biopython) + ("python-click" ,python-click) + ("python-cytoolz" ,python-cytoolz) + ("python-dask" ,python-dask) + ("python-h5py" ,python-h5py) + ("python-multiprocess" ,python-multiprocess) + ("python-pandas" ,python-pandas) + ("python-pyfaidx" ,python-pyfaidx) + ("python-pypairix" ,python-pypairix) + ("python-pysam" ,python-pysam) + ("python-scipy" ,python-scipy))) + (native-inputs + `(("python-mock" ,python-mock) + ("python-nose" ,python-nose) + ("python-numpydoc" ,python-numpydoc) + ("python-sphinx" ,python-sphinx))) + (home-page "https://github.com/mirnylab/cooler") + (synopsis "Sparse binary format for genomic interaction matrices") + (description + "Cooler is a support library for a sparse, compressed, binary persistent +storage format, called @code{cool}, used to store genomic interaction data, +such as Hi-C contact matrices.") + (license license:bsd-3))) + +(define-public python-hicexplorer + (package + (name "python-hicexplorer") + (version "2.1.4") + (source + (origin + ;; The latest version is not available on Pypi. + (method git-fetch) + (uri (git-reference + (url "https://github.com/deeptools/HiCExplorer.git") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0q5gpbzmrkvygqgw524q36b4nrivcmyi5v194vsx0qw7b3gcmq08")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'loosen-up-requirements + (lambda _ + (substitute* "setup.py" + (("==") ">=")) + #t))))) + (propagated-inputs + `(("python-biopython" ,python-biopython) + ("python-configparser" ,python-configparser) + ("python-cooler" ,python-cooler) + ("python-future" ,python-future) + ("python-intervaltree" ,python-intervaltree) + ("python-jinja2" ,python-jinja2) + ("python-matplotlib" ,python-matplotlib) + ("python-numpy" ,python-numpy) + ("python-pandas" ,python-pandas) + ("python-pybigwig" ,python-pybigwig) + ("python-pysam" ,python-pysam) + ("python-scipy" ,python-scipy) + ("python-six" ,python-six) + ("python-tables" ,python-tables) + ("python-unidecode" ,python-unidecode))) + (home-page "http://hicexplorer.readthedocs.io") + (synopsis "Process, analyze and visualize Hi-C data") + (description + "HiCExplorer is a powerful and easy to use set of tools to process, +normalize and visualize Hi-C data. HiCExplorer facilitates the creation of +contact matrices, correction of contacts, TAD detection, A/B compartments, +merging, reordering or chromosomes, conversion from different formats +including cooler and detection of long-range contacts. Moreover, it allows +the visualization of multiple contact matrices along with other types of data +like genes, compartments, ChIP-seq coverage tracks (and in general any type of +genomic scores), long range contacts and the visualization of viewpoints.") + (license license:gpl3))) + +(define-public python-pygenometracks + (package + (name "python-pygenometracks") + (version "2.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "pyGenomeTracks" version)) + (sha256 + (base32 + "1fws6bqsyy9kj3qiabhkqx4wd4i775gsxnhszqd3zg7w67sc1ic5")))) + (build-system python-build-system) + (propagated-inputs + `(("python-configparser" ,python-configparser) + ("python-future" ,python-future) + ("python-hicexplorer" ,python-hicexplorer) + ("python-intervaltree" ,python-intervaltree) + ("python-matplotlib" ,python-matplotlib) + ("python-numpy" ,python-numpy) + ("python-pybigwig" ,python-pybigwig))) + (native-inputs + `(("python-pytest" ,python-pytest))) + (home-page "https://pygenometracks.readthedocs.io") + (synopsis "Program and library to plot beautiful genome browser tracks") + (description + "This package aims to produce high-quality genome browser tracks that +are highly customizable. Currently, it is possible to plot: bigwig, bed (many +options), bedgraph, links (represented as arcs), and Hi-C matrices. +pyGenomeTracks can make plots with or without Hi-C data.") + (license license:gpl3+))) + +(define-public python-hic2cool + (package + (name "python-hic2cool") + (version "0.4.2") + (source + (origin + (method url-fetch) + (uri (pypi-uri "hic2cool" version)) + (sha256 + (base32 + "0xy6mhfns2lzib1kcr6419jjp6pmh0qx8z8na55lmiwn0ds8q9cl")))) + (build-system python-build-system) + (arguments '(#:tests? #f)) ; no tests included + (propagated-inputs + `(("python-cooler" ,python-cooler))) + (home-page "https://github.com/4dn-dcic/hic2cool") + (synopsis "Converter for .hic and .cool files") + (description + "This package provides a converter between @code{.hic} files (from +juicer) and single-resolution or multi-resolution @code{.cool} files (for +cooler). Both @code{hic} and @code{cool} files describe Hi-C contact +matrices.") + (license license:expat))) + +(define-public r-pore + (package + (name "r-pore") + (version "0.24") + (source + (origin + (method url-fetch) + (uri + (string-append "mirror://sourceforge/rpore/" version + "/poRe_" version ".tar.gz")) + (sha256 + (base32 "0pih9nljbv8g4x8rkk29i7aqq681b782r5s5ynp4nw9yzqnmmksv")))) + (properties `((upstream-name . "poRe"))) + (build-system r-build-system) + (propagated-inputs + `(("r-bit64" ,r-bit64) + ("r-data-table" ,r-data-table) + ("r-rhdf5" ,r-rhdf5) + ("r-shiny" ,r-shiny) + ("r-svdialogs" ,r-svdialogs))) + (home-page "https://sourceforge.net/projects/rpore/") + (synopsis "Visualize Nanopore sequencing data") + (description + "This package provides graphical user interfaces to organize and visualize Nanopore +sequencing data.") + ;; This is free software but the license variant is unclear: + ;; <https://github.com/mw55309/poRe_docs/issues/10>. + (license license:bsd-3))) + +(define-public r-xbioc + (let ((revision "1") + (commit "f798c187e376fd1ba27abd559f47bbae7e3e466b")) + (package + (name "r-xbioc") + (version (git-version "0.1.15" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/renozao/xbioc.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "03hffh2f6z71y6l6dqpa5cql3hdaw7zigdi8sm2dzgx379k9rgrr")))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-assertthat" ,r-assertthat) + ("r-biobase" ,r-biobase) + ("r-biocinstaller" ,r-biocinstaller) + ("r-digest" ,r-digest) + ("r-pkgmaker" ,r-pkgmaker) + ("r-plyr" ,r-plyr) + ("r-reshape2" ,r-reshape2) + ("r-stringr" ,r-stringr))) + (home-page "https://github.com/renozao/xbioc/") + (synopsis "Extra base functions for Bioconductor") + (description "This package provides extra utility functions to perform +common tasks in the analysis of omics data, leveraging and enhancing features +provided by Bioconductor packages.") + (license license:gpl3+)))) + +(define-public r-cssam + (let ((revision "1") + (commit "9ec58c982fa551af0d80b1a266890d92954833f2")) + (package + (name "r-cssam") + (version (git-version "1.4" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/shenorrLab/csSAM.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "128syf9v39gk0z3ip000qpsjbg6l1siyq6c8b0hz41dzg5achyb3")))) + (build-system r-build-system) + (propagated-inputs + `(("r-formula" ,r-formula) + ("r-ggplot2" ,r-ggplot2) + ("r-pkgmaker" ,r-pkgmaker) + ("r-plyr" ,r-plyr) + ("r-rngtools" ,r-rngtools) + ("r-scales" ,r-scales))) + (home-page "https://github.com/shenorrLab/csSAM/") + (synopsis "Cell type-specific statistical analysis of microarray") + (description "This package implements the method csSAM that computes +cell-specific differential expression from measured cell proportions using +SAM.") + ;; Any version + (license license:lgpl2.1+)))) + +(define-public r-bseqsc + (let ((revision "1") + (commit "fef3f3e38dcf3df37103348b5780937982b43b98")) + (package + (name "r-bseqsc") + (version (git-version "1.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/shenorrLab/bseqsc.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1prw13wa20f7wlc3gkkls66n1kxz8d28qrb8icfqdwdnnv8w5qg8")))) + (build-system r-build-system) + (propagated-inputs + `(("r-abind" ,r-abind) + ("r-annotationdbi" ,r-annotationdbi) + ("r-biobase" ,r-biobase) + ("r-cssam" ,r-cssam) + ("r-dplyr" ,r-dplyr) + ("r-e1071" ,r-e1071) + ("r-edger" ,r-edger) + ("r-ggplot2" ,r-ggplot2) + ("r-nmf" ,r-nmf) + ("r-openxlsx" ,r-openxlsx) + ("r-pkgmaker" ,r-pkgmaker) + ("r-plyr" ,r-plyr) + ("r-preprocesscore" ,r-preprocesscore) + ("r-rngtools" ,r-rngtools) + ("r-scales" ,r-scales) + ("r-stringr" ,r-stringr) + ("r-xbioc" ,r-xbioc))) + (home-page "https://github.com/shenorrLab/bseqsc") + (synopsis "Deconvolution of bulk sequencing experiments using single cell data") + (description "BSeq-sc is a bioinformatics analysis pipeline that +leverages single-cell sequencing data to estimate cell type proportion and +cell type-specific gene expression differences from RNA-seq data from bulk +tissue samples. This is a companion package to the publication \"A +single-cell transcriptomic map of the human and mouse pancreas reveals inter- +and intra-cell population structure.\" Baron et al. Cell Systems (2016) +@url{https://www.ncbi.nlm.nih.gov/pubmed/27667365}.") + (license license:gpl2+)))) + +(define-public porechop + ;; The recommended way to install is to clone the git repository + ;; https://github.com/rrwick/Porechop#installation + (let ((commit "289d5dca4a5fc327f97b3f8cecb68ecaf1014861") + (revision "1")) + (package + (name "porechop") + (version (git-version "0.2.3" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/rrwick/Porechop.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "05ps43gig0d3ia9x5lj84lb00hbsl6ba9n7y7jz927npxbr2ym23")))) + (build-system python-build-system) + (home-page "https://github.com/rrwick/porechop") + (synopsis "Finding, trimming or splitting adapters, in Oxford Nanopore reads") + (description + "The porechop package is a tool for finding and removing adapters from Oxford +Nanopore reads. Adapters on the ends of reads are trimmed off, and when a read +has an adapter in its middle, it is treated as chimeric and chopped into +separate reads. Porechop performs thorough alignments to effectively find +adapters, even at low sequence identity. Porechop also supports demultiplexing +of Nanopore reads that were barcoded with the Native Barcoding Kit, PCR +Barcoding Kit or Rapid Barcoding Kit.") + (license license:gpl3+)))) + +(define-public poretools + ;; The latest release was in 2016 and the latest commit is from 2017 + ;; the recommended way to install is to clone the git repository + ;; https://poretools.readthedocs.io/en/latest/content/installation.html + (let ((commit "e426b1f09e86ac259a00c261c79df91510777407") + (revision "1")) + (package + (name "poretools") + (version (git-version "0.6.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/arq5x/poretools.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0bglj833wxpp3cq430p1d3xp085ls221js2y90w7ir2x5ay8l7am")))) + (build-system python-build-system) + ;; requires python >=2.7, <3.0, and the same for python dependencies + (arguments `(#:python ,python-2)) + (inputs + `(("hdf5" ,hdf5))) + (propagated-inputs + `(("python-dateutil" ,python2-dateutil) + ("python-h5py" ,python2-h5py) + ("python-matplotlib" ,python2-matplotlib) + ("python-pandas" ,python2-pandas) + ("python-seaborn" ,python2-seaborn))) + (home-page "https://poretools.readthedocs.io") + (synopsis "Toolkit for working with nanopore sequencing data") + (description + "The MinION from Oxford Nanopore Technologies is a nanopore sequencer. +This @code{poretools} package is a flexible toolkit for exploring datasets +generated by nanopore sequencing devices for the purposes of quality control and +downstream analysis. Poretools operates directly on the native FAST5, a variant +of the Hierarchical Data Format (HDF5) standard.") + (license license:expat)))) + +(define-public r-absfiltergsea + (package + (name "r-absfiltergsea") + (version "1.5.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "AbsFilterGSEA" version)) + (sha256 + (base32 "15srxkxsvn38kd5frdrwfdf0ad8gskrd0h01wmdf9hglq8fjrp7w")))) + (properties `((upstream-name . "AbsFilterGSEA"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-deseq" ,r-deseq) + ("r-limma" ,r-limma) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo))) + (home-page "https://cran.r-project.org/web/packages/AbsFilterGSEA/") + (synopsis "Improved false positive control of gene-permuting with absolute filtering") + (description + "This package provides a function that performs gene-permuting of a gene-set +enrichment analysis (GSEA) calculation with or without the absolute filtering. + Without filtering, users can perform (original) two-tailed or one-tailed +absolute GSEA.") + (license license:gpl2))) + +(define-public jamm + (package + (name "jamm") + (version "1.0.7.5") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/mahmoudibrahim/JAMM.git") + (commit (string-append "JAMMv" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0ls889jcma1ch9h21jjhnkadgszgqj41842hhcjh6cg88f85qf3i")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; there are none + #:phases + (modify-phases %standard-phases + (delete 'configure) + (replace 'build + (lambda* (#:key inputs outputs #:allow-other-keys) + (substitute* "JAMM.sh" + (("^sPath=.*") + (string-append ""))) + #t)) + (replace 'install + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (libexec (string-append out "/libexec/jamm")) + (bin (string-append out "/bin"))) + (substitute* '("JAMM.sh" + "SignalGenerator.sh") + (("^sPath=.*") + (string-append "sPath=\"" libexec "\"\n"))) + (for-each (lambda (file) + (install-file file libexec)) + (list "bincalculator.r" + "peakfinder.r" + "peakhelper.r" + "signalmaker.r" + "xcorr.r" + "xcorrhelper.r" + ;; Perl scripts + "peakfilter.pl" + "readshifter.pl")) + + (for-each + (lambda (script) + (chmod script #o555) + (install-file script bin) + (wrap-program (string-append bin "/" script) + `("PATH" ":" prefix + (,(string-append (assoc-ref inputs "coreutils") "/bin") + ,(string-append (assoc-ref inputs "gawk") "/bin") + ,(string-append (assoc-ref inputs "perl") "/bin") + ,(string-append (assoc-ref inputs "r-minimal") "/bin"))) + `("PERL5LIB" ":" prefix (,(getenv "PERL5LIB"))) + `("R_LIBS_SITE" ":" prefix (,(getenv "R_LIBS_SITE"))))) + (list "JAMM.sh" "SignalGenerator.sh"))) + #t))))) + (inputs + `(("bash" ,bash) + ("coreutils" ,coreutils) + ("gawk" ,gawk) + ("perl" ,perl) + ("r-minimal" ,r-minimal) + ;;("r-parallel" ,r-parallel) + ("r-signal" ,r-signal) + ("r-mclust" ,r-mclust))) + (home-page "https://github.com/mahmoudibrahim/JAMM") + (synopsis "Peak finder for NGS datasets") + (description + "JAMM is a peak finder for next generation sequencing datasets (ChIP-Seq, +ATAC-Seq, DNase-Seq, etc.) that can integrate replicates and assign peak +boundaries accurately. JAMM is applicable to both broad and narrow +datasets.") + (license license:gpl3+))) + +(define-public ngless + (package + (name "ngless") + (version "0.9.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://gitlab.com/ngless/ngless.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0mc2gi7h4lx74zylvyp76mvc0w6706j858ii9vlgzqsw6acpr117")))) + (build-system haskell-build-system) + (arguments + `(#:haddock? #f ; The haddock phase fails with: NGLess/CmdArgs.hs:20:1: + ; error: parse error on input import + ; import Options.Applicative + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'create-cabal-file + (lambda _ (invoke "hpack") #t)) + ;; These tools are expected to be installed alongside ngless. + (add-after 'install 'link-tools + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) + (symlink (string-append (assoc-ref inputs "prodigal") + "/bin/prodigal") + (string-append bin "ngless-" ,version "-prodigal")) + (symlink (string-append (assoc-ref inputs "minimap2") + "/bin/minimap2") + (string-append bin "ngless-" ,version "-minimap2")) + (symlink (string-append (assoc-ref inputs "samtools") + "/bin/samtools") + (string-append bin "ngless-" ,version "-samtools")) + (symlink (string-append (assoc-ref inputs "bwa") + "/bin/bwa") + (string-append bin "ngless-" ,version "-bwa")) + #t)))))) + (inputs + `(("prodigal" ,prodigal) + ("bwa" ,bwa) + ("samtools" ,samtools) + ("minimap2" ,minimap2) + ("ghc-aeson" ,ghc-aeson) + ("ghc-ansi-terminal" ,ghc-ansi-terminal) + ("ghc-async" ,ghc-async) + ("ghc-atomic-write" ,ghc-atomic-write) + ("ghc-bytestring-lexing" ,ghc-bytestring-lexing) + ("ghc-chart" ,ghc-chart) + ("ghc-chart-cairo" ,ghc-chart-cairo) + ("ghc-conduit" ,ghc-conduit) + ("ghc-conduit-algorithms" ,ghc-conduit-algorithms) + ("ghc-conduit-combinators" ,ghc-conduit-combinators) + ("ghc-conduit-extra" ,ghc-conduit-extra) + ("ghc-configurator" ,ghc-configurator) + ("ghc-convertible" ,ghc-convertible) + ("ghc-data-default" ,ghc-data-default) + ("ghc-double-conversion" ,ghc-double-conversion) + ("ghc-edit-distance" ,ghc-edit-distance) + ("ghc-either" ,ghc-either) + ("ghc-errors" ,ghc-errors) + ("ghc-extra" ,ghc-extra) + ("ghc-filemanip" ,ghc-filemanip) + ("ghc-file-embed" ,ghc-file-embed) + ("ghc-gitrev" ,ghc-gitrev) + ("ghc-hashtables" ,ghc-hashtables) + ("ghc-http-conduit" ,ghc-http-conduit) + ("ghc-inline-c" ,ghc-inline-c) + ("ghc-inline-c-cpp" ,ghc-inline-c-cpp) + ("ghc-intervalmap" ,ghc-intervalmap) + ("ghc-missingh" ,ghc-missingh) + ("ghc-optparse-applicative" ,ghc-optparse-applicative) + ("ghc-parsec" ,ghc-parsec) + ("ghc-regex" ,ghc-regex) + ("ghc-safe" ,ghc-safe) + ("ghc-safeio" ,ghc-safeio) + ("ghc-strict" ,ghc-strict) + ("ghc-tar" ,ghc-tar) + ("ghc-text" ,ghc-text) + ("ghc-unliftio" ,ghc-unliftio) + ("ghc-unliftio-core" ,ghc-unliftio-core) + ("ghc-vector" ,ghc-vector) + ("ghc-yaml" ,ghc-yaml) + ("ghc-zlib" ,ghc-zlib))) + (propagated-inputs + `(("r-r6" ,r-r6) + ("r-hdf5r" ,r-hdf5r) + ("r-iterators" ,r-iterators) + ("r-itertools" ,r-itertools) + ("r-matrix" ,r-matrix))) + (native-inputs + `(("ghc-hpack" ,ghc-hpack) + ("ghc-quickcheck" ,ghc-quickcheck) + ("ghc-test-framework" ,ghc-test-framework) + ("ghc-test-framework-hunit",ghc-test-framework-hunit) + ("ghc-test-framework-quickcheck2" ,ghc-test-framework-quickcheck2) + ("ghc-test-framework-th" ,ghc-test-framework-th))) + (home-page "https://gitlab.com/ngless/ngless") + (synopsis "DSL for processing next-generation sequencing data") + (description "Ngless is a domain-specific language for +@dfn{next-generation sequencing} (NGS) data processing.") + (license license:expat))) + +(define-public filtlong + ;; The recommended way to install is to clone the git repository + ;; https://github.com/rrwick/Filtlong#installation + ;; and the lastest release is more than nine months old + (let ((commit "d1bb46dfe8bc7efe6257b5ce222c04bfe8aedaab") + (revision "1")) + (package + (name "filtlong") + (version (git-version "0.2.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/rrwick/Filtlong.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1xr92r820x8qlkcr3b57iw223yq8vjgyi42jr79w2xgw47qzr575")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; no check target + #:phases + (modify-phases %standard-phases + (delete 'configure) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin")) + (scripts (string-append out "/share/filtlong/scripts"))) + (install-file "bin/filtlong" bin) + (install-file "scripts/histogram.py" scripts) + (install-file "scripts/read_info_histograms.sh" scripts)) + #t)) + (add-after 'install 'wrap-program + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (path (getenv "PYTHONPATH"))) + (wrap-program (string-append out + "/share/filtlong/scripts/histogram.py") + `("PYTHONPATH" ":" prefix (,path)))) + #t)) + (add-before 'check 'patch-tests + (lambda _ + (substitute* "scripts/read_info_histograms.sh" + (("awk") (which "gawk"))) + #t))))) + (inputs + `(("gawk" ,gawk) ;for read_info_histograms.sh + ("python" ,python-2) ;required for histogram.py + ("zlib" ,zlib))) + (home-page "https://github.com/rrwick/Filtlong/") + (synopsis "Tool for quality filtering of Nanopore and PacBio data") + (description + "The Filtlong package is a tool for filtering long reads by quality. +It can take a set of long reads and produce a smaller, better subset. It uses +both read length (longer is better) and read identity (higher is better) when +choosing which reads pass the filter.") + (license (list license:gpl3 ;filtlong + license:asl2.0))))) ;histogram.py + +(define-public nanopolish + ;; The recommended way to install is to clone the git repository + ;; <https://github.com/jts/nanopolish#installing-a-particular-release>. + ;; Also, the differences between release and current version seem to be + ;; significant. + (let ((commit "50e8b5cc62f9b46f5445f5c5e8c5ab7263ea6d9d") + (revision "1")) + (package + (name "nanopolish") + (version (git-version "0.10.2" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/jts/nanopolish.git") + (commit commit) + (recursive? #t))) + (file-name (git-file-name name version)) + (sha256 + (base32 "09j5gz57yr9i34a27vbl72i4g8syv2zzgmsfyjq02yshmnrvkjs6")))) + (build-system gnu-build-system) + (arguments + `(#:make-flags + `("HDF5=noinstall" "EIGEN=noinstall" "HTS=noinstall" "CC=gcc") + #:tests? #f ; no check target + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'find-eigen + (lambda* (#:key inputs #:allow-other-keys) + (setenv "CPATH" + (string-append (assoc-ref inputs "eigen") + "/include/eigen3")) + #t)) + (delete 'configure) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin")) + (scripts (string-append out "/share/nanopolish/scripts"))) + + (install-file "nanopolish" bin) + (for-each (lambda (file) (install-file file scripts)) + (find-files "scripts" ".*")) + #t))) + (add-after 'install 'wrap-programs + (lambda* (#:key outputs #:allow-other-keys) + (for-each (lambda (file) + (wrap-program file `("PYTHONPATH" ":" prefix (,path)))) + (find-files "/share/nanopolish/scripts" "\\.py")) + (for-each (lambda (file) + (wrap-program file `("PERL5LIB" ":" prefix (,path)))) + (find-files "/share/nanopolish/scripts" "\\.pl")) + #t))))) + (inputs + `(("eigen" ,eigen) + ("hdf5" ,hdf5) + ("htslib" ,htslib) + ("perl" ,perl) + ("python" ,python) + ("python-biopython" ,python-biopython) + ("python-numpy" ,python-numpy) + ("python-pysam" ,python-pysam) + ("python-scikit-learn" , python-scikit-learn) + ("python-scipy" ,python-scipy) + ("zlib" ,zlib))) + (home-page "https://github.com/jts/nanopolish") + (synopsis "Signal-level analysis of Oxford Nanopore sequencing data") + (description + "This package analyses the Oxford Nanopore sequencing data at signal-level. +Nanopolish can calculate an improved consensus sequence for a draft genome +assembly, detect base modifications, call SNPs (Single nucleotide +polymorphisms) and indels with respect to a reference genome and more.") + (license license:expat)))) |