diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 658 |
1 files changed, 341 insertions, 317 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1e04081ceb..96ea07bdc4 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1332,7 +1332,7 @@ 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 @@ -1340,13 +1340,12 @@ 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) @@ -1383,7 +1382,7 @@ 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 @@ -1450,13 +1449,14 @@ 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) @@ -1474,40 +1474,38 @@ 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") @@ -1597,19 +1595,19 @@ 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") @@ -1896,31 +1894,18 @@ 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 @@ -1934,22 +1919,46 @@ 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))) @@ -2044,15 +2053,15 @@ 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") @@ -2082,14 +2091,14 @@ trees (phylogenies) and characters.") (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") @@ -2101,7 +2110,7 @@ with Python.") (define-public deeptools (package (name "deeptools") - (version "3.1.2") + (version "3.1.3") (source (origin (method git-fetch) (uri (git-reference @@ -2110,7 +2119,7 @@ with Python.") (file-name (git-file-name name version)) (sha256 (base32 - "06fdpp6cg3xiwryxjhixvfysl4z0ps1crjgia587qa9ikqpsa7fd")))) + "1vggnf52g6q2vifdl4cyi7s2fnfqq0ky2zrkj5zv2qfzsc3p3siw")))) (build-system python-build-system) (arguments `(#:phases @@ -2146,42 +2155,42 @@ 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 @@ -2195,14 +2204,14 @@ 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 @@ -2230,13 +2239,14 @@ 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 @@ -2264,106 +2274,102 @@ 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) @@ -2379,6 +2385,7 @@ 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") @@ -2474,17 +2481,16 @@ 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 @@ -2492,17 +2498,13 @@ 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") @@ -2535,31 +2537,30 @@ 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)))))) @@ -2606,38 +2607,39 @@ 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 @@ -2646,7 +2648,7 @@ 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 @@ -3741,75 +3743,48 @@ 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 @@ -5601,25 +5576,38 @@ 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/") @@ -5746,14 +5734,15 @@ 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")) @@ -5763,11 +5752,11 @@ 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")) @@ -5776,7 +5765,7 @@ 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 @@ -5787,6 +5776,41 @@ 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") |