diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 274 |
1 files changed, 256 insertions, 18 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e277f890a1..7b3838d36f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1,3 +1,4 @@ + ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2014, 2015, 2016 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2015, 2016 Ben Woodcroft <donttrustben@gmail.com> @@ -39,6 +40,8 @@ #:use-module (gnu packages boost) #:use-module (gnu packages compression) #:use-module (gnu packages cpio) + #:use-module (gnu packages curl) + #:use-module (gnu packages doxygen) #:use-module (gnu packages file) #:use-module (gnu packages gawk) #:use-module (gnu packages gcc) @@ -1080,6 +1083,52 @@ preparation protocols.") other types of unwanted sequence from high-throughput sequencing reads.") (license license:expat))) +(define-public libbigwig + (package + (name "libbigwig") + (version "0.1.4") + (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")) + (sha256 + (base32 + "098rjh35pi4a9q83n8wiwvyzykjqj6l8q189p1xgfw4ghywdlvw1")))) + (build-system gnu-build-system) + (arguments + `(#:test-target "test" + #: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)))))) + (inputs + `(("zlib" ,zlib) + ("curl" ,curl))) + (native-inputs + `(("doxygen" ,doxygen))) + (home-page "https://github.com/dpryan79/libBigWig") + (synopsis "C library for handling bigWig files") + (description + "This package provides a C library for parsing local and remote BigWig +files.") + (license license:expat))) + (define-public deeptools (package (name "deeptools") @@ -1741,7 +1790,7 @@ particular, reads spanning multiple exons.") (base32 "0djmgc0pfli0jilfx8hql1axhwhqxqb8rxg2r5rg07aw73sfs5nx")))) (build-system gnu-build-system) - (native-inputs `(("perl", perl))) + (native-inputs `(("perl" ,perl))) (home-page "http://hmmer.janelia.org") (synopsis "Biosequence analysis using profile hidden Markov models") (description @@ -1773,6 +1822,8 @@ HMMs).") ;; Numpy needs to be propagated when htseq is used as a Python library. (propagated-inputs `(("python-numpy" ,python2-numpy))) + (inputs + `(("python-pysam" ,python2-pysam))) (native-inputs `(("python-setuptools" ,python2-setuptools))) (home-page "http://www-huber.embl.de/users/anders/HTSeq/") @@ -1964,15 +2015,13 @@ command, or queried for specific k-mers with @code{jellyfish query}.") (define-public macs (package (name "macs") - (version "2.1.0.20140616") + (version "2.1.0.20151222") (source (origin (method url-fetch) - (uri (string-append - "https://pypi.python.org/packages/source/M/MACS2/MACS2-" - version ".tar.gz")) + (uri (pypi-uri "MACS2" version)) (sha256 (base32 - "11lmiw6avqhwn75sn59g4lfkrr2kk20r3rgfbx9xfqb8rg9mi2n6")))) + "1r2hcz6irhcq7lwbafjks98jbn34hv05avgbdjnp6w6mlfjkf8x5")))) (build-system python-build-system) (arguments `(#:python ,python-2 ; only compatible with Python 2.7 @@ -2359,7 +2408,7 @@ generated using the PacBio Iso-Seq protocol.") (define-public prodigal (package (name "prodigal") - (version "2.6.2") + (version "2.6.3") (source (origin (method url-fetch) (uri (string-append @@ -2368,7 +2417,7 @@ generated using the PacBio Iso-Seq protocol.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0m8sb0fg6lmxrlpzna0am6svbnlmd3dckrhgzxxgb3gxr5fyj284")))) + "17srxkqd3jc77xk15pfbgg1a9xahqg7337w95mrsia7mpza4l2c9")))) (build-system gnu-build-system) (arguments `(#:tests? #f ;no check target @@ -3311,6 +3360,61 @@ features; exactSNP: a SNP caller that discovers SNPs by testing signals against local background noises.") (license license:gpl3+))) +(define-public stringtie + (package + (name "stringtie") + (version "1.2.1") + (source (origin + (method url-fetch) + (uri (string-append "http://ccb.jhu.edu/software/stringtie/dl/" + "stringtie-" version ".tar.gz")) + (sha256 + (base32 + "1cqllsc1maq4kh92isi8yadgzbmnf042hlnalpk3y59aph1z3bfz")) + (modules '((guix build utils))) + (snippet + '(begin + (delete-file-recursively "samtools-0.1.18") + #t)))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ;no test suite + #:phases + (modify-phases %standard-phases + ;; no configure script + (delete 'configure) + (add-before 'build 'use-system-samtools + (lambda _ + (substitute* "Makefile" + (("stringtie: \\$\\{BAM\\}/libbam\\.a") + "stringtie: ")) + (substitute* '("gclib/GBam.h" + "gclib/GBam.cpp") + (("#include \"(bam|sam|kstring).h\"" _ header) + (string-append "#include <samtools/" header ".h>"))) + #t)) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) + (install-file "stringtie" bin) + #t)))))) + (inputs + `(("samtools" ,samtools-0.1) + ("zlib" ,zlib))) + (home-page "http://ccb.jhu.edu/software/stringtie/") + (synopsis "Transcript assembly and quantification for RNA-Seq data") + (description + "StringTie is a fast and efficient assembler of RNA-Seq sequence +alignments into potential transcripts. It uses a novel network flow algorithm +as well as an optional de novo assembly step to assemble and quantitate +full-length transcripts representing multiple splice variants for each gene +locus. Its input can include not only the alignments of raw reads used by +other transcript assemblers, but also alignments of longer sequences that have +been assembled from those reads. To identify differentially expressed genes +between experiments, StringTie's output can be processed either by the +Cuffdiff or Ballgown programs.") + (license license:artistic2.0))) + (define-public vcftools (package (name "vcftools") @@ -3355,7 +3459,7 @@ data in the form of VCF files.") (define-public vsearch (package (name "vsearch") - (version "1.4.1") + (version "1.10.0") (source (origin (method url-fetch) @@ -3365,7 +3469,7 @@ data in the form of VCF files.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0b1359wbzgb2cm04h7dq05v80vik88hnsv298xxd1q1f2q4ydni7")) + "1i3bad7gnn2y3a1yfixzshd99xdkjc8w5bxzgifpysc6jiljwvb5")) (modules '((guix build utils))) (snippet '(begin @@ -3375,14 +3479,24 @@ data in the form of VCF files.") -O3 -mtune=native -Wall -Wsign-compare") (string-append "AM_CXXFLAGS=-lcityhash" " -O3 -Wall -Wsign-compare")) - (("^__top_builddir__bin_vsearch_SOURCES = cityhash/city.h \\\\") + (("^__top_builddir__bin_vsearch_SOURCES = city.h \\\\") "__top_builddir__bin_vsearch_SOURCES = \\") - (("^cityhash/config.h \\\\") "\\") - (("^cityhash/city.cc \\\\") "\\")) + (("^city.h \\\\") "\\") + (("^citycrc.h \\\\") "\\") + (("^libcityhash_a.*") "") + (("noinst_LIBRARIES = libcpu_sse2.a libcpu_ssse3.a \ +libcityhash.a") + "noinst_LIBRARIES = libcpu_sse2.a libcpu_ssse3.a") + (("__top_builddir__bin_vsearch_LDADD = libcpu_ssse3.a \ +libcpu_sse2.a libcityhash.a") + "__top_builddir__bin_vsearch_LDADD = libcpu_ssse3.a \ +libcpu_sse2.a -lcityhash")) (substitute* "src/vsearch.h" - (("^\\#include \"cityhash/city.h\"") - "#include <city.h>")) - (delete-file-recursively "src/cityhash") + (("^\\#include \"city.h\"") "#include <city.h>") + (("^\\#include \"citycrc.h\"") "#include <citycrc.h>")) + (delete-file "src/city.h") + (delete-file "src/citycrc.h") + (delete-file "src/city.cc") #t)))) (build-system gnu-build-system) (arguments @@ -3725,13 +3839,13 @@ on Bioconductor or which replace R functions.") (define-public r-annotationdbi (package (name "r-annotationdbi") - (version "1.32.2") + (version "1.32.3") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationDbi" version)) (sha256 (base32 - "08ncdjvq0l44kqyiv32kn9wnbw1xgfb6qjfzfbjpqrcfp1jygz9j")))) + "1v6x62hgys5827yg2xayjrd9xawbayzm6wy0q4vxh1s6yxc9bklj")))) (properties `((upstream-name . "AnnotationDbi"))) (build-system r-build-system) @@ -4043,6 +4157,25 @@ 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 "1.48.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "graph" version)) + (sha256 + (base32 + "16w75rji3kv24gfv44w66y1a2y75ax26rl470y3ypna0ndc3rrcd")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics))) + (home-page "http://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") @@ -4061,6 +4194,7 @@ information about the latest version of the Gene Ontologies.") ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-go-db" ,r-go-db) + ("r-graph" ,r-graph) ("r-sparsem" ,r-sparsem))) (home-page "http://bioconductor.org/packages/topGO") (synopsis "Enrichment analysis for gene ontology") @@ -4191,6 +4325,110 @@ genomic feature data as long as it has minimal information on the locations of genomic intervals. In addition, it can use BAM or BigWig files as input.") (license license:artistic2.0))) +(define-public r-org-hs-eg-db + (package + (name "r-org-hs-eg-db") + (version "3.2.3") + (source (origin + (method url-fetch) + ;; We cannot use bioconductor-uri here because this tarball is + ;; located under "data/annotation/" instead of "bioc/". + (uri (string-append "http://www.bioconductor.org/packages/" + "release/data/annotation/src/contrib/" + "org.Hs.eg.db_" version ".tar.gz")) + (sha256 + (base32 + "0xicgkbh6xkvs74s1piafqac63dyz2ycdyil4pj4ghhxx2sabm6p")))) + (properties + `((upstream-name . "org.Hs.eg.db"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi))) + (home-page "http://www.bioconductor.org/packages/org.Hs.eg.db/") + (synopsis "Genome wide annotation for Human") + (description + "This package provides mappings from Entrez gene identifiers to various +annotations for the human genome.") + (license license:artistic2.0))) + +(define-public r-org-ce-eg-db + (package + (name "r-org-ce-eg-db") + (version "3.2.3") + (source (origin + (method url-fetch) + ;; We cannot use bioconductor-uri here because this tarball is + ;; located under "data/annotation/" instead of "bioc/". + (uri (string-append "http://www.bioconductor.org/packages/" + "release/data/annotation/src/contrib/" + "org.Ce.eg.db_" version ".tar.gz")) + (sha256 + (base32 + "1d0lx00ybq34yqs6mziaa0lrh77xm0ggsmi76g6k95f77gi7m1sw")))) + (properties + `((upstream-name . "org.Ce.eg.db"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi))) + (home-page "http://www.bioconductor.org/packages/org.Ce.eg.db/") + (synopsis "Genome wide annotation for Worm") + (description + "This package provides mappings from Entrez gene identifiers to various +annotations for the genome of the model worm Caenorhabditis elegans.") + (license license:artistic2.0))) + +(define-public r-org-dm-eg-db + (package + (name "r-org-dm-eg-db") + (version "3.2.3") + (source (origin + (method url-fetch) + ;; We cannot use bioconductor-uri here because this tarball is + ;; located under "data/annotation/" instead of "bioc/". + (uri (string-append "http://www.bioconductor.org/packages/" + "release/data/annotation/src/contrib/" + "org.Dm.eg.db_" version ".tar.gz")) + (sha256 + (base32 + "0mib46c7nr00l7mh290n383za9hyl91a1dc6jhjbk884jmxaxyz6")))) + (properties + `((upstream-name . "org.Dm.eg.db"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi))) + (home-page "http://www.bioconductor.org/packages/org.Dm.eg.db/") + (synopsis "Genome wide annotation for Fly") + (description + "This package provides mappings from Entrez gene identifiers to various +annotations for the genome of the model fruit fly Drosophila melanogaster.") + (license license:artistic2.0))) + +(define-public r-org-mm-eg-db + (package + (name "r-org-mm-eg-db") + (version "3.2.3") + (source (origin + (method url-fetch) + ;; We cannot use bioconductor-uri here because this tarball is + ;; located under "data/annotation/" instead of "bioc/". + (uri (string-append "http://www.bioconductor.org/packages/" + "release/data/annotation/src/contrib/" + "org.Mm.eg.db_" version ".tar.gz")) + (sha256 + (base32 + "0wh1pm3npdg7070875kfgiid3bqkz3q7rq6snhk6bxfvph00298y")))) + (properties + `((upstream-name . "org.Mm.eg.db"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi))) + (home-page "http://www.bioconductor.org/packages/org.Mm.eg.db/") + (synopsis "Genome wide annotation for Mouse") + (description + "This package provides mappings from Entrez gene identifiers to various +annotations for the genome of the model mouse Mus musculus.") + (license license:artistic2.0))) + (define-public r-qtl (package (name "r-qtl") |