diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 460 |
1 files changed, 355 insertions, 105 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 51e3df6d81..7c573e1626 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -44,6 +44,7 @@ #:use-module (gnu packages linux) #:use-module (gnu packages machine-learning) #:use-module (gnu packages maths) + #:use-module (gnu packages mpi) #:use-module (gnu packages ncurses) #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) @@ -347,15 +348,14 @@ provide a coordinated and extensible framework to do computational biology.") (define-public python-biopython (package (name "python-biopython") - (version "1.65") + (version "1.66") (source (origin (method url-fetch) - (uri (string-append - "http://biopython.org/DIST/biopython-" - version ".tar.gz")) + ;; use PyPi rather than biopython.org to ease updating + (uri (pypi-uri "biopython" version)) (sha256 (base32 - "13m8s9jkrw40zvdp1rl709n6lmgdh4f52aann7gzr6sfp0fwhg26")))) + "1gdv92593klimg22icf5j9by7xiq86jnwzkpz4abaa05ylkdf6hp")))) (build-system python-build-system) (inputs `(("python-numpy" ,python-numpy))) @@ -524,6 +524,89 @@ confidence to have in an alignment.") license:lgpl2.0+ license:asl2.0)))) +(define-public bless + (package + (name "bless") + (version "1p02") + (source (origin + (method url-fetch) + (uri (string-append "mirror://sourceforge/bless-ec/bless.v" + version ".tgz")) + (sha256 + (base32 + "0rm0gw2s18dqwzzpl3c2x1z05ni2v0xz5dmfk3d33j6g4cgrlrdd")) + (modules '((guix build utils))) + (snippet + `(begin + ;; Remove bundled boost, pigz, zlib, and .git directory + ;; FIXME: also remove bundled sources for google-sparsehash, + ;; murmurhash3, kmc once packaged. + (delete-file-recursively "boost") + (delete-file-recursively "pigz") + (delete-file-recursively "zlib") + (delete-file-recursively ".git") + #t)))) + (build-system gnu-build-system) + (arguments + '(#:tests? #f ;no "check" target + #:make-flags + (list (string-append "ZLIB=" + (assoc-ref %build-inputs "zlib") + "/lib/libz.a") + (string-append "LDFLAGS=" + (string-join '("-lboost_filesystem" + "-lboost_system" + "-lboost_iostreams" + "-lz" + "-fopenmp" + "-std=c++11")))) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'do-not-build-bundled-pigz + (lambda* (#:key inputs outputs #:allow-other-keys) + (substitute* "Makefile" + (("cd pigz/pigz-2.3.3; make") "")) + #t)) + (add-after 'unpack 'patch-paths-to-executables + (lambda* (#:key inputs outputs #:allow-other-keys) + (substitute* "parse_args.cpp" + (("kmc_binary = .*") + (string-append "kmc_binary = \"" + (assoc-ref outputs "out") + "/bin/kmc\";")) + (("pigz_binary = .*") + (string-append "pigz_binary = \"" + (assoc-ref inputs "pigz") + "/bin/pigz\";"))) + #t)) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) + (for-each (lambda (file) + (install-file file bin)) + '("bless" "kmc/bin/kmc")) + #t))) + (delete 'configure)))) + (native-inputs + `(("perl" ,perl))) + (inputs + `(("openmpi" ,openmpi) + ("boost" ,boost) + ("pigz" ,pigz) + ("zlib" ,zlib))) + (supported-systems '("x86_64-linux")) + (home-page "http://sourceforge.net/p/bless-ec/wiki/Home/") + (synopsis "Bloom-filter-based error correction tool for NGS reads") + (description + "@dfn{Bloom-filter-based error correction solution for high-throughput +sequencing reads} (BLESS) uses a single minimum-sized bloom filter is a +correction tool for genomic reads produced by @dfn{Next-generation +sequencing} (NGS). BLESS produces accurate correction results with much less +memory compared with previous solutions and is also able to tolerate a higher +false-positive rate. BLESS can extend reads like DNA assemblers to correct +errors at the end of reads.") + (license license:gpl3+))) + (define-public bowtie (package (name "bowtie") @@ -805,15 +888,16 @@ time.") (define-public crossmap (package (name "crossmap") - (version "0.1.6") + (version "0.2.1") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/crossmap/CrossMap-" version ".tar.gz")) (sha256 (base32 - "163hi5gjgij6cndxlvbkp5jjwr0k4wbm9im6d2210278q7k9kpnp")) - ;; patch has been sent upstream already + "07y179f63d7qnzdvkqcziwk9bs3k4zhp81q392fp1hwszjdvy22f")) + ;; This patch has been sent upstream already and is available + ;; for download from Sourceforge, but it has not been merged. (patches (list (search-patch "crossmap-allow-system-pysam.patch"))) (modules '((guix build utils))) @@ -1028,7 +1112,7 @@ data and settings.") ("perl" ,perl))) (native-inputs `(("unzip" ,unzip))) - (home-page "http://www.ncbi.nlm.nih.gov/books/NBK179288") + (home-page "http://www.ncbi.nlm.nih.gov/books/NBK179288/") (synopsis "Tools for accessing the NCBI's set of databases") (description "Entrez Direct (EDirect) is a method for accessing the National Center @@ -1089,6 +1173,51 @@ analysis (from RNA-Seq), transcription factor binding quantification in ChIP-Seq, and analysis of metagenomic data.") (license license:artistic2.0))) +(define-public express-beta-diversity + (package + (name "express-beta-diversity") + (version "1.0.7") + (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")) + (sha256 + (base32 + "1djvdlmqvjf6h0zq7w36y8cl5cli6rgj86x65znl48agnwmzxfxr")))) + (build-system gnu-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (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)) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") + "/bin"))) + (mkdir-p bin) + (copy-file "scripts/convertToEBD.py" + (string-append bin "/convertToEBD.py")) + (copy-file "bin/ExpressBetaDiversity" + (string-append bin "/ExpressBetaDiversity")) + #t)))))) + (inputs + `(("python" ,python-2))) + (home-page "http://kiwi.cs.dal.ca/Software/ExpressBetaDiversity") + (synopsis "Taxon- and phylogenetic-based beta diversity measures") + (description + "Express Beta Diversity (EBD) calculates ecological beta diversity +(dissimilarity) measures between biological communities. EBD implements a +variety of diversity measures including those that make use of phylogenetic +similarity of community members.") + (license license:gpl3+))) + (define-public fasttree (package (name "fasttree") @@ -1328,6 +1457,9 @@ estimates transcript expression.") `(("perl" ,perl) ("python" ,python) ("zlib" ,zlib))) + ;; Non-portable SSE instructions are used so building fails on platforms + ;; other than x86_64. + (supported-systems '("x86_64-linux")) (home-page "http://ccb.jhu.edu/software/hisat/index.shtml") (synopsis "Hierarchical indexing for spliced alignment of transcripts") (description @@ -1382,9 +1514,11 @@ HMMs).") "1i85ppf2j2lj12m0x690qq5nn17xxk23pbbx2c83r8ayb5wngzwv")))) (build-system python-build-system) (arguments `(#:python ,python-2)) ; only Python 2 is supported - (inputs - `(("python-numpy" ,python2-numpy) - ("python-setuptools" ,python2-setuptools))) + ;; Numpy needs to be propagated when htseq is used as a Python library. + (propagated-inputs + `(("python-numpy" ,python2-numpy))) + (native-inputs + `(("python-setuptools" ,python2-setuptools))) (home-page "http://www-huber.embl.de/users/anders/HTSeq/") (synopsis "Analysing high-throughput sequencing data with Python") (description @@ -1838,19 +1972,25 @@ the phenotype as it models the data.") (license license:asl2.0))) (define-public pbtranscript-tofu - (let ((commit "c7bbd5472")) + (let ((commit "8f5467fe6")) (package (name "pbtranscript-tofu") - (version (string-append "0.4.1." commit)) + (version (string-append "2.2.3." commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/PacificBiosciences/cDNA_primer.git") (commit commit))) - (file-name (string-append name "-" version ".tar.gz")) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "148xkzi689c49g6fdhckp6mnmj2qhjdf1j4wifm6ja7ij95d7fxx")))) + "1lgnpi35ihay42qx0b6yl3kkgra723i413j33kvs0kvs61h82w0f")) + (modules '((guix build utils))) + (snippet + '(begin + ;; remove bundled Cython sources + (delete-file "pbtranscript-tofu/pbtranscript/Cython-0.20.1.tar.gz") + #t)))) (build-system python-build-system) (arguments `(#:python ,python-2 @@ -1860,34 +2000,29 @@ the phenotype as it models the data.") #:configure-flags '("--single-version-externally-managed" "--record=pbtranscript-tofu.txt") #:phases - (alist-cons-after - 'unpack 'enter-directory-and-clean-up - (lambda _ - (chdir "pbtranscript-tofu/pbtranscript/") - ;; Delete clutter - (delete-file-recursively "dist/") - (delete-file-recursively "build/") - (delete-file-recursively "setuptools_cython-0.2.1-py2.6.egg/") - (delete-file-recursively "pbtools.pbtranscript.egg-info") - (delete-file "Cython-0.20.1.tar.gz") - (delete-file "setuptools_cython-0.2.1-py2.7.egg") - (delete-file "setuptools_cython-0.2.1.tar.gz") - (delete-file "setup.cfg") - (for-each delete-file - (find-files "." "\\.so$")) - ;; files should be writable for install phase - (for-each (lambda (f) (chmod f #o755)) - (find-files "." "\\.py$"))) - %standard-phases))) + (modify-phases %standard-phases + (add-after 'unpack 'enter-directory + (lambda _ + (chdir "pbtranscript-tofu/pbtranscript/") + #t)) + ;; With setuptools version 18.0 and later this setup.py hack causes + ;; a build error, so we disable it. + (add-after 'enter-directory 'patch-setuppy + (lambda _ + (substitute* "setup.py" + (("if 'setuptools.extension' in sys.modules:") + "if False:")) + #t))))) (inputs - `(("python-cython" ,python2-cython) - ("python-numpy" ,python2-numpy) + `(("python-numpy" ,python2-numpy) ("python-bx-python" ,python2-bx-python) ("python-networkx" ,python2-networkx) ("python-scipy" ,python2-scipy) - ("python-pbcore" ,python2-pbcore))) + ("python-pbcore" ,python2-pbcore) + ("python-h5py" ,python2-h5py))) (native-inputs - `(("python-nose" ,python2-nose) + `(("python-cython" ,python2-cython) + ("python-nose" ,python2-nose) ("python-setuptools" ,python2-setuptools))) (home-page "https://github.com/PacificBiosciences/cDNA_primer") (synopsis "Analyze transcriptome data generated with the Iso-Seq protocol") @@ -2149,10 +2284,57 @@ viewer.") (string-append bin "/samtools"))))) (delete 'patch-tests))))))) +(define-public mosaik + (let ((commit "5c25216d")) + (package + (name "mosaik") + (version "2.2.30") + (source (origin + ;; There are no release tarballs nor tags. + (method git-fetch) + (uri (git-reference + (url "https://github.com/wanpinglee/MOSAIK.git") + (commit commit))) + (file-name (string-append name "-" version)) + (sha256 + (base32 + "17gj3s07cm77r41z92awh0bim7w7q7fbn0sf5nkqmcm1vw052qgw")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; no tests + #:make-flags (list "CC=gcc") + #:phases + (modify-phases %standard-phases + (replace 'configure + (lambda _ (chdir "src") #t)) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") + "/bin"))) + (mkdir-p bin) + (copy-recursively "../bin" bin) + #t)))))) + (inputs + `(("perl" ,perl) + ("zlib" ,zlib))) + (supported-systems '("x86_64-linux")) + (home-page "https://code.google.com/p/mosaik-aligner/") + (synopsis "Map nucleotide sequence reads to reference genomes") + (description + "MOSAIK is a program for mapping second and third-generation sequencing +reads to a reference genome. MOSAIK can align reads generated by all the +major sequencing technologies, including Illumina, Applied Biosystems SOLiD, +Roche 454, Ion Torrent and Pacific BioSciences SMRT.") + ;; MOSAIK is released under the GPLv2+ with the exception of third-party + ;; code released into the public domain: + ;; 1. fastlz by Ariya Hidayat - http://www.fastlz.org/ + ;; 2. MD5 implementation - RSA Data Security, RFC 1321 + (license (list license:gpl2+ license:public-domain))))) + (define-public ngs-sdk (package (name "ngs-sdk") - (version "1.1.1") + (version "1.2.2") (source (origin (method url-fetch) @@ -2162,7 +2344,7 @@ viewer.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1x58gpm574n0xmk2a98gmikbgycq78ia0bvnb42k5ck34fmd5v8y")))) + "0rvq61zfw2h9jcz6a33b9xrl20r7s5a9rldvv6rs2qy42khpmf5j")))) (build-system gnu-build-system) (arguments `(#:parallel-build? #f ; not supported @@ -2206,26 +2388,8 @@ simultaneously.") (srfi srfi-26)) ,@(package-arguments ngs-sdk)) ((#:phases phases) - `(alist-cons-after - 'enter-dir 'fix-java-symlink-installation - (lambda _ - ;; Only replace the version suffix, not the version number in - ;; the directory name. Reported here: - ;; https://github.com/ncbi/ngs/pull/4 - (substitute* "Makefile.java" - (((string-append "\\$\\(subst " - "(\\$\\(VERSION[^\\)]*\\))," - "(\\$\\([^\\)]+\\))," - "(\\$\\([^\\)]+\\)|\\$\\@)" - "\\)") - _ pattern replacement target) - (string-append "$(patsubst " - "%" pattern "," - "%" replacement "," - target ")")))) - (alist-replace - 'enter-dir (lambda _ (chdir "ngs-java") #t) - ,phases)))))) + `(modify-phases ,phases + (replace 'enter-dir (lambda _ (chdir "ngs-java") #t))))))) (inputs `(("jdk" ,icedtea6 "jdk") ("ngs-sdk" ,ngs-sdk))) @@ -2234,7 +2398,7 @@ simultaneously.") (define-public ncbi-vdb (package (name "ncbi-vdb") - (version "2.4.5-5") + (version "2.5.4") (source (origin (method url-fetch) @@ -2244,7 +2408,7 @@ simultaneously.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1cj8nk6if8sqagv20vx36v566fdvhcaadf0x1ycnbgql6chbs6vy")))) + "1rcnyc4xkdfcjww2i0s0qrbapys0cxbjcx2sy3qkpslf9f400fgj")))) (build-system gnu-build-system) (arguments `(#:parallel-build? #f ; not supported @@ -2254,20 +2418,6 @@ simultaneously.") 'configure (lambda* (#:key inputs outputs #:allow-other-keys) (let ((out (assoc-ref outputs "out"))) - ;; Only replace the version suffix, not the version number in the - ;; directory name; fixed in commit 4dbba5c6a809 (no release yet). - (substitute* "setup/konfigure.perl" - (((string-append "\\$\\(subst " - "(\\$\\(VERSION[^\\)]*\\))," - "(\\$\\([^\\)]+\\))," - "(\\$\\([^\\)]+\\)|\\$\\@)" - "\\)") - _ pattern replacement target) - (string-append "$(patsubst " - "%" pattern "," - "%" replacement "," - target ")"))) - ;; Override include path for libmagic (substitute* "setup/package.prl" (("name => 'magic', Include => '/usr/include'") @@ -2383,49 +2533,95 @@ subsequent visualization, annotation and storage of results.") ;; LGPLv2.1+ (license (list license:gpl2 license:lgpl2.1+)))) +(define-public smithlab-cpp + (let ((revision "1") + (commit "728a097")) + (package + (name "smithlab-cpp") + (version (string-append "0." revision "." commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/smithlabcode/smithlab_cpp.git") + (commit commit))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 + "0d476lmj312xk77kr9fzrv7z1bv96yfyx0w7y62ycmnfbx32ll74")))) + (build-system gnu-build-system) + (arguments + `(#:modules ((guix build gnu-build-system) + (guix build utils) + (srfi srfi-26)) + #:tests? #f ;no "check" target + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'use-samtools-headers + (lambda _ + (substitute* '("SAM.cpp" + "SAM.hpp") + (("sam.h") "samtools/sam.h")) + #t)) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (lib (string-append out "/lib")) + (include (string-append out "/include/smithlab-cpp"))) + (mkdir-p lib) + (mkdir-p include) + (for-each (cut install-file <> lib) + (find-files "." "\\.o$")) + (for-each (cut install-file <> include) + (find-files "." "\\.hpp$"))) + #t)) + (delete 'configure)))) + (inputs + `(("samtools" ,samtools-0.1) + ("zlib" ,zlib))) + (home-page "https://github.com/smithlabcode/smithlab_cpp") + (synopsis "C++ helper library for functions used in Smith lab projects") + (description + "Smithlab CPP is a C++ library that includes functions used in many of +the Smith lab bioinformatics projects, such as a wrapper around Samtools data +structures, classes for genomic regions, mapped sequencing reads, etc.") + (license license:gpl3+)))) + (define-public preseq (package (name "preseq") - (version "1.0.2") + (version "2.0") (source (origin (method url-fetch) - (uri - (string-append "http://smithlabresearch.org/downloads/preseq-" - version ".tar.bz2")) + (uri (string-append "https://github.com/smithlabcode/" + "preseq/archive/v" version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) (sha256 - (base32 "0r7sw07p6nv8ygvc17gd78lisbw5336v3vhs86b5wv8mw3pwqksc")) - (patches (list (search-patch "preseq-1.0.2-install-to-PREFIX.patch") - (search-patch "preseq-1.0.2-link-with-libbam.patch"))) + (base32 "08r684l50pnxjpvmhzjgqq56yv9rfw90k8vx0nsrnrzk8mf9hsdq")) (modules '((guix build utils))) (snippet ;; Remove bundled samtools. - '(delete-file-recursively "preseq-master/samtools")))) + '(delete-file-recursively "samtools")))) (build-system gnu-build-system) (arguments `(#:tests? #f ;no "check" target #:phases (modify-phases %standard-phases - (add-after - 'unpack 'enter-dir - (lambda _ - (chdir "preseq-master") - #t)) - (add-after - 'enter-dir 'use-samtools-headers - (lambda _ - (substitute* '("smithlab_cpp/SAM.cpp" - "smithlab_cpp/SAM.hpp") - (("sam.h") "samtools/sam.h")) - #t)) (delete 'configure)) - #:make-flags (list (string-append "PREFIX=" - (assoc-ref %outputs "out")) - (string-append "LIBBAM=" - (assoc-ref %build-inputs "samtools") - "/lib/libbam.a")))) + #:make-flags + (list (string-append "PREFIX=" + (assoc-ref %outputs "out")) + (string-append "LIBBAM=" + (assoc-ref %build-inputs "samtools") + "/lib/libbam.a") + (string-append "SMITHLAB_CPP=" + (assoc-ref %build-inputs "smithlab-cpp") + "/lib") + "PROGS=preseq" + "INCLUDEDIRS=$(SMITHLAB_CPP)/../include/smithlab-cpp $(SAMTOOLS_DIR)"))) (inputs `(("gsl" ,gsl) ("samtools" ,samtools-0.1) + ("smithlab-cpp" ,smithlab-cpp) ("zlib" ,zlib))) (home-page "http://smithlabresearch.org/software/preseq/") (synopsis "Program for analyzing library complexity") @@ -2442,7 +2638,7 @@ complexity samples.") (define-public sra-tools (package (name "sra-tools") - (version "2.4.5-5") + (version "2.5.4") (source (origin (method url-fetch) @@ -2452,7 +2648,7 @@ complexity samples.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "11nrnvz7a012f4iryf0wiwrid0h111grsfxbxa9j51h3f2xbvgns")))) + "1rxxc8a34g70jcaa2j8sys2x93amlbc24k7az39wldhkzgi96825")))) (build-system gnu-build-system) (arguments `(#:parallel-build? #f ; not supported @@ -2595,6 +2791,43 @@ BioPython in a convenient way. Instead of having a big mess of scripts, there is one that takes arguments.") (license license:gpl3))) +(define-public snap-aligner + (package + (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")) + (sha256 + (base32 + "1vnsjwv007k1fl1q7d681kbwn6bc66cgw6h16hym6gvyy71qv2ly")))) + (build-system gnu-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (delete 'configure) + (replace 'check (lambda _ (zero? (system* "./unit_tests")))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin"))) + (mkdir-p bin) + (install-file "snap-aligner" bin) + (install-file "SNAPCommand" bin) + #t)))))) + (native-inputs + `(("zlib" ,zlib))) + (home-page "http://snap.cs.berkeley.edu/") + (synopsis "Short read DNA sequence aligner") + (description + "SNAP is a fast and accurate aligner for short DNA reads. It is +optimized for modern read lengths of 100 bases or higher, and takes advantage +of these reads to align data quickly through a hash-based indexing scheme.") + (license license:asl2.0))) + (define-public star (package (name "star") @@ -2657,7 +2890,24 @@ sequences.") (build-system gnu-build-system) (arguments `(#:tests? #f ;no "check" target - #:make-flags '("-f" "Makefile.Linux") + ;; The CC and CCFLAGS variables are set to contain a lot of x86_64 + ;; optimizations by default, so we override these flags such that x86_64 + ;; flags are only added when the build target is an x86_64 system. + #:make-flags + (list (let ((system ,(or (%current-target-system) + (%current-system))) + (flags '("-ggdb" "-fomit-frame-pointer" + "-ffast-math" "-funroll-loops" + "-fmessage-length=0" + "-O9" "-Wall" "-DMAKE_FOR_EXON" + "-DMAKE_STANDALONE" + "-DSUBREAD_VERSION=\\\"${SUBREAD_VERSION}\\\"")) + (flags64 '("-mmmx" "-msse" "-msse2" "-msse3"))) + (if (string-prefix? "x86_64" system) + (string-append "CCFLAGS=" (string-join (append flags flags64))) + (string-append "CCFLAGS=" (string-join flags)))) + "-f" "Makefile.Linux" + "CC=gcc ${CCFLAGS}") #:phases (alist-cons-after 'unpack 'enter-dir |