diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 1006 |
1 files changed, 978 insertions, 28 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1214a0b708..b29ca67dbd 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -19,23 +19,68 @@ (define-module (gnu packages bioinformatics) #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) + #:use-module (guix utils) #:use-module (guix download) + #:use-module (guix git-download) #:use-module (guix build-system gnu) #:use-module (guix build-system cmake) #:use-module (guix build-system python) #:use-module (guix build-system trivial) #:use-module (gnu packages) #:use-module (gnu packages base) + #:use-module (gnu packages boost) #:use-module (gnu packages compression) + #:use-module (gnu packages file) #:use-module (gnu packages java) + #:use-module (gnu packages linux) + #:use-module (gnu packages maths) #:use-module (gnu packages ncurses) #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) + #:use-module (gnu packages popt) + #:use-module (gnu packages protobuf) #:use-module (gnu packages python) + #:use-module (gnu packages statistics) + #:use-module (gnu packages swig) #:use-module (gnu packages tbb) + #:use-module (gnu packages textutils) #:use-module (gnu packages vim) + #:use-module (gnu packages xml) #:use-module (gnu packages zip)) +(define-public bamtools + (package + (name "bamtools") + (version "2.3.0") + (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")) + (sha256 + (base32 + "1brry29bw2xr2l9pqn240rkqwayg85b8qq78zk2zs6nlspk4d018")))) + (build-system cmake-build-system) + (arguments + `(#:tests? #f ;no "check" target + #:phases + (modify-phases %standard-phases + (add-before + 'configure 'set-ldflags + (lambda* (#:key outputs #:allow-other-keys) + (setenv "LDFLAGS" + (string-append + "-Wl,-rpath=" + (assoc-ref outputs "out") "/lib/bamtools"))))))) + (inputs `(("zlib" ,zlib))) + (home-page "https://github.com/pezmaster31/bamtools") + (synopsis "C++ API and command-line toolkit for working with BAM data") + (description + "BamTools provides both a C++ API and a command-line toolkit for handling +BAM files.") + (license license:expat))) + (define-public bedops (package (name "bedops") @@ -177,6 +222,39 @@ pybedtools extends BEDTools by offering feature-level manipulations from with Python.") (license license:gpl2+))) +(define-public python-biopython + (package + (name "python-biopython") + (version "1.65") + (source (origin + (method url-fetch) + (uri (string-append + "http://biopython.org/DIST/biopython-" + version ".tar.gz")) + (sha256 + (base32 + "13m8s9jkrw40zvdp1rl709n6lmgdh4f52aann7gzr6sfp0fwhg26")))) + (build-system python-build-system) + (inputs + `(("python-numpy" ,python-numpy))) + (native-inputs + `(("python-setuptools" ,python2-setuptools))) + (home-page "http://biopython.org/") + (synopsis "Tools for biological computation in Python") + (description + "Biopython is a set of tools for biological computation including parsers +for bioinformatics files into Python data structures; interfaces to common +bioinformatics programs; a standard sequence class and tools for performing +common operations on them; code to perform data classification; code for +dealing with alignments; code making it easy to split up parallelizable tasks +into separate processes; and more.") + (license (license:non-copyleft "http://www.biopython.org/DIST/LICENSE")))) + +(define-public python2-biopython + (package (inherit (package-with-python2 python-biopython)) + (inputs + `(("python2-numpy" ,python2-numpy))))) + (define-public bowtie (package (name "bowtie") @@ -285,6 +363,41 @@ and more accurate. BWA-MEM also has better performance than BWA-backtrack for 70-100bp Illumina reads.") (license license:gpl3+))) +(define-public python2-bx-python + (package + (name "python2-bx-python") + (version "0.7.2") + (source (origin + (method url-fetch) + (uri (string-append + "https://pypi.python.org/packages/source/b/bx-python/bx-python-" + version ".tar.gz")) + (sha256 + (base32 + "0ld49idhc5zjdvbhvjq1a2qmpjj7h5v58rqr25dzmfq7g34b50xh")) + (modules '((guix build utils))) + (snippet + '(substitute* "setup.py" + ;; remove dependency on outdated "distribute" module + (("^from distribute_setup import use_setuptools") "") + (("^use_setuptools\\(\\)") ""))))) + (build-system python-build-system) + (arguments + `(#:tests? #f ;tests fail because test data are not included + #:python ,python-2)) + (inputs + `(("python-numpy" ,python2-numpy) + ("zlib" ,zlib))) + (native-inputs + `(("python-nose" ,python2-nose) + ("python-setuptools" ,python2-setuptools))) + (home-page "http://bitbucket.org/james_taylor/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 clipper (package (name "clipper") @@ -323,6 +436,30 @@ and more accurate. BWA-MEM also has better performance than BWA-backtrack for "CLIPper is a tool to define peaks in CLIP-seq datasets.") (license license:gpl2))) +(define-public clustal-omega + (package + (name "clustal-omega") + (version "1.2.1") + (source (origin + (method url-fetch) + (uri (string-append + "http://www.clustal.org/omega/clustal-omega-" + version ".tar.gz")) + (sha256 + (base32 + "02ibkx0m0iwz8nscg998bh41gg251y56cgh86bvyrii5m8kjgwqf")))) + (build-system gnu-build-system) + (inputs + `(("argtable" ,argtable))) + (home-page "http://www.clustal.org/omega/") + (synopsis "Multiple sequence aligner for protein and DNA/RNA") + (description + "Clustal-Omega is a general purpose multiple sequence alignment (MSA) +program for protein and DNA/RNA. It produces high quality MSAs and is capable +of handling data-sets of hundreds of thousands of sequences in reasonable +time.") + (license license:gpl2+))) + (define-public crossmap (package (name "crossmap") @@ -365,6 +502,123 @@ 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 cutadapt + (package + (name "cutadapt") + (version "1.8") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/marcelm/cutadapt/archive/v" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "161bp87y6gd6r5bmvjpn2b1k942i3fizfpa139f0jn6jv1wcp5h5")))) + (build-system python-build-system) + (arguments + ;; tests must be run after install + `(#:phases (alist-cons-after + 'install 'check + (lambda* (#:key inputs outputs #:allow-other-keys) + (setenv "PYTHONPATH" + (string-append + (getenv "PYTHONPATH") + ":" (assoc-ref outputs "out") + "/lib/python" + (string-take (string-take-right + (assoc-ref inputs "python") 5) 3) + "/site-packages")) + (zero? (system* "nosetests" "-P" "tests"))) + (alist-delete 'check %standard-phases)))) + (native-inputs + `(("python-cython" ,python-cython) + ("python-nose" ,python-nose) + ("python-setuptools" ,python-setuptools))) + (home-page "https://code.google.com/p/cutadapt/") + (synopsis "Remove adapter sequences from nucleotide sequencing reads") + (description + "Cutadapt finds and removes adapter sequences, primers, poly-A tails and +other types of unwanted sequence from high-throughput sequencing reads.") + (license license:expat))) + +(define-public express + (package + (name "express") + (version "1.5.1") + (source (origin + (method url-fetch) + (uri + (string-append + "http://bio.math.berkeley.edu/eXpress/downloads/express-" + version "/express-" version "-src.tgz")) + (sha256 + (base32 + "03rczxd0gjp2l1jxcmjfmf5j94j77zqyxa6x063zsc585nj40n0c")))) + (build-system cmake-build-system) + (arguments + `(#:tests? #f ;no "check" target + #:phases + (alist-cons-after + 'unpack 'use-shared-boost-libs-and-set-bamtools-paths + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "CMakeLists.txt" + (("set\\(Boost_USE_STATIC_LIBS ON\\)") + "set(Boost_USE_STATIC_LIBS OFF)") + (("\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/bamtools/include") + (string-append (assoc-ref inputs "bamtools") "/include/bamtools"))) + (substitute* "src/CMakeLists.txt" + (("\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/\\.\\./bamtools/lib") + (string-append (assoc-ref inputs "bamtools") "/lib/bamtools"))) + #t) + %standard-phases))) + (inputs + `(("boost" ,boost) + ("bamtools" ,bamtools) + ("protobuf" ,protobuf) + ("zlib" ,zlib))) + (home-page "http://bio.math.berkeley.edu/eXpress") + (synopsis "Streaming quantification for high-throughput genomic sequencing") + (description + "eXpress is a streaming tool for quantifying the abundances of a set of +target sequences from sampled subsequences. Example applications include +transcript-level RNA-Seq quantification, allele-specific/haplotype expression +analysis (from RNA-Seq), transcription factor binding quantification in +ChIP-Seq, and analysis of metagenomic data.") + (license license:artistic2.0))) + +(define-public fastx-toolkit + (package + (name "fastx-toolkit") + (version "0.0.14") + (source (origin + (method url-fetch) + (uri + (string-append + "https://github.com/agordon/fastx_toolkit/releases/download/" + version "/fastx_toolkit-" version ".tar.bz2")) + (sha256 + (base32 + "01jqzw386873sr0pjp1wr4rn8fsga2vxs1qfmicvx1pjr72007wy")))) + (build-system gnu-build-system) + (inputs + `(("libgtextutils" ,libgtextutils))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (home-page "http://hannonlab.cshl.edu/fastx_toolkit/") + (synopsis "Tools for FASTA/FASTQ file preprocessing") + (description + "The FASTX-Toolkit is a collection of command line tools for Short-Reads +FASTA/FASTQ files preprocessing. + +Next-Generation sequencing machines usually produce FASTA or FASTQ files, +containing multiple short-reads sequences. The main processing of such +FASTA/FASTQ files is mapping the sequences to reference genomes. However, it +is sometimes more productive to preprocess the files before mapping the +sequences to the genome---manipulating the sequences to produce better mapping +results. The FASTX-Toolkit tools perform some of these preprocessing tasks.") + (license license:agpl3+))) + (define-public flexbar (package (name "flexbar") @@ -379,15 +633,20 @@ file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.") "13jaykc3y1x8y5nn9j8ljnb79s5y51kyxz46hdmvvjj6qhyympmf")))) (build-system cmake-build-system) (arguments - `(;; There is no test target, although there is a directory containing - ;; test data and scripts (launched by flexbar_validate.sh). - #:tests? #f - #:configure-flags (list + `(#:configure-flags (list (string-append "-DFLEXBAR_BINARY_DIR=" (assoc-ref %outputs "out") "/bin/")) #:phases - (alist-delete 'install %standard-phases))) + (alist-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"))) + (alist-delete 'install %standard-phases)))) (inputs `(("tbb" ,tbb) ("zlib" ,zlib))) @@ -405,6 +664,57 @@ supports next-generation sequencing data in fasta/q and csfasta/q format from Illumina, Roche 454, and the SOLiD platform.") (license license:gpl3))) +(define-public grit + (package + (name "grit") + (version "2.0.2") + (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")) + (sha256 + (base32 + "157in84dj70wimbind3x7sy1whs3h57qfgcnj2s6lrd38fbrb7mj")))) + (build-system python-build-system) + (arguments + `(#:python ,python-2 + #:phases + (alist-cons-after + 'unpack 'generate-from-cython-sources + (lambda* (#:key inputs outputs #:allow-other-keys) + ;; Delete these C files to force fresh generation from pyx sources. + (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/" + "']"))) #t) + %standard-phases))) + (inputs + `(("python-scipy" ,python2-scipy) + ("python-numpy" ,python2-numpy) + ("python-pysam" ,python2-pysam) + ("python-networkx" ,python2-networkx))) + (native-inputs + `(("python-cython" ,python2-cython) + ("python-setuptools" ,python2-setuptools))) + (home-page "http://grit-bio.org") + (synopsis "Tool for integrative analysis of RNA-seq type assays") + (description + "GRIT is designed to use RNA-seq, TES, and TSS data to build and quantify +full length transcript models. When none of these data sources are available, +GRIT can be run by providing a candidate set of TES or TSS sites. In +addition, GRIT can merge in reference junctions and gene boundaries. GRIT can +also be run in quantification mode, where it uses a provided GTF file and just +estimates transcript expression.") + (license license:gpl3+))) + (define-public hisat (package (name "hisat") @@ -615,6 +925,172 @@ RNA-Seq, the MISO model uses Bayesian inference to compute the probability that a read originated from a particular isoform.") (license license:gpl2))) +(define-public python2-pbcore + (package + (name "python2-pbcore") + (version "0.9.3") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/PacificBiosciences/pbcore/archive/" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1z46rwjac93jm87cbj2zgjg6qvsgs65140wkbbxsvxps7ai4pm09")))) + (build-system python-build-system) + (arguments `(#:python ,python-2)) ; pbcore requires Python 2.7 + (inputs + `(("python-cython" ,python2-cython) + ("python-numpy" ,python2-numpy) + ("python-pysam" ,python2-pysam) + ("python-h5py" ,python2-h5py))) + (native-inputs + `(("python-setuptools" ,python2-setuptools))) + (home-page "http://pacificbiosciences.github.io/pbcore/") + (synopsis "Library for reading and writing PacBio data files") + (description + "The pbcore package provides Python APIs for interacting with PacBio data +files and writing bioinformatics applications.") + (license license:bsd-3))) + +(define-public pbtranscript-tofu + (let ((commit "c7bbd5472")) + (package + (name "pbtranscript-tofu") + (version (string-append "0.4.1." 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")) + (sha256 + (base32 + "148xkzi689c49g6fdhckp6mnmj2qhjdf1j4wifm6ja7ij95d7fxx")))) + (build-system python-build-system) + (arguments + `(#:python ,python-2 + ;; With standard flags, the install phase attempts to create a zip'd + ;; egg file, and fails with an error: 'ZIP does not support timestamps + ;; before 1980' + #: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))) + (inputs + `(("python-cython" ,python2-cython) + ("python-numpy" ,python2-numpy) + ("python-bx-python" ,python2-bx-python) + ("python-networkx" ,python2-networkx) + ("python-scipy" ,python2-scipy) + ("python-pbcore" ,python2-pbcore))) + (native-inputs + `(("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") + (description + "pbtranscript-tofu contains scripts to analyze transcriptome data +generated using the PacBio Iso-Seq protocol.") + (license license:bsd-3)))) + +(define-public rsem + (package + (name "rsem") + (version "1.2.20") + (source + (origin + (method url-fetch) + (uri + (string-append "http://deweylab.biostat.wisc.edu/rsem/src/rsem-" + version ".tar.gz")) + (sha256 + (base32 "0nzdc0j0hjllhsd5f2xli95dafm3nawskigs140xzvjk67xh0r9q")) + (patches (list (search-patch "rsem-makefile.patch"))) + (modules '((guix build utils))) + (snippet + '(begin + ;; remove bundled copy of boost + (delete-file-recursively "boost") + #t)))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ;no "check" target + #: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)) + (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) + (copy-file file + (string-append bin (basename file)))) + (find-files "." "rsem-.*")) + (copy-file "rsem_perl_utils.pm" + (string-append perl "/rsem_perl_utils.pm"))) + #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))))) + (inputs + `(("boost" ,boost) + ("ncurses" ,ncurses) + ("r" ,r) + ("perl" ,perl) + ("samtools" ,samtools-0.1) + ("zlib" ,zlib))) + (home-page "http://deweylab.biostat.wisc.edu/rsem/") + (synopsis "Estimate gene expression levels from RNA-Seq data") + (description + "RSEM is a software package for estimating gene and isoform expression +levels from RNA-Seq data. The RSEM package provides a user-friendly +interface, supports threads for parallel computation of the EM algorithm, +single-end and paired-end read data, quality scores, variable-length reads and +RSPD estimation. In addition, it provides posterior mean and 95% credibility +interval estimates for expression levels. For visualization, it can generate +BAM and Wiggle files in both transcript-coordinate and genomic-coordinate.") + (license license:gpl3+))) + (define-public rseqc (package (name "rseqc") @@ -626,7 +1102,7 @@ that a read originated from a particular isoform.") (string-append "mirror://sourceforge/rseqc/" version "/RSeQC-" version ".tar.gz")) (sha256 - (base32 "09rf0x9d6apjja5l01cgprj7vigpw6kiqhy34ibwwlxil0db0ri4")) + (base32 "15ly0254yi032qzkdplg00q144qfdsd986gh62829rl5bkxhj330")) (modules '((guix build utils))) (snippet '(begin @@ -680,32 +1156,31 @@ distribution, coverage uniformity, strand specificity, etc.") ;; systems. #:tests? ,(string=? (or (%current-system) (%current-target-system)) "x86_64-linux") - #:make-flags (list (string-append "prefix=" (assoc-ref %outputs "out"))) + #:make-flags (list "LIBCURSES=-lncurses" + (string-append "prefix=" (assoc-ref %outputs "out"))) #:phases (alist-cons-after 'unpack - 'patch-makefile-curses - (lambda _ - (substitute* "Makefile" - (("-lcurses") "-lncurses"))) + 'patch-tests + (lambda* (#:key inputs #:allow-other-keys) + (let ((bash (assoc-ref inputs "bash"))) + (substitute* "test/test.pl" + ;; The test script calls out to /bin/bash + (("/bin/bash") + (string-append bash "/bin/bash")) + ;; There are two failing tests upstream relating to the "stats" + ;; subcommand in test_usage_subcommand ("did not have Usage" + ;; and "usage did not mention samtools stats"), so we disable + ;; them. + (("(test_usage_subcommand\\(.*\\);)" cmd) + (string-append "unless ($subcommand eq 'stats') {" cmd "};"))))) (alist-cons-after - 'unpack - 'patch-tests - (lambda* (#:key inputs #:allow-other-keys) - (let ((bash (assoc-ref inputs "bash"))) - (substitute* "test/test.pl" - ;; The test script calls out to /bin/bash - (("/bin/bash") - (string-append bash "/bin/bash")) - ;; There are two failing tests upstream relating to the "stats" - ;; subcommand in test_usage_subcommand ("did not have Usage" - ;; and "usage did not mention samtools stats"), so we disable - ;; them. - (("(test_usage_subcommand\\(.*\\);)" cmd) - (string-append "unless ($subcommand eq 'stats') {" cmd "};"))))) - (alist-delete - 'configure - %standard-phases))))) + 'install 'install-library + (lambda* (#:key outputs #:allow-other-keys) + (let ((lib (string-append (assoc-ref outputs "out") "/lib"))) + (mkdir-p lib) + (copy-file "libbam.a" (string-append lib "/libbam.a")))) + (alist-delete 'configure %standard-phases))))) (native-inputs `(("pkg-config" ,pkg-config))) (inputs `(("ncurses" ,ncurses) ("perl" ,perl) @@ -720,6 +1195,296 @@ variant calling (in conjunction with bcftools), and a simple alignment viewer.") (license license:expat))) +(define-public samtools-0.1 + ;; This is the most recent version of the 0.1 line of samtools. The input + ;; and output formats differ greatly from that used and produced by samtools + ;; 1.x and is still used in many bioinformatics pipelines. + (package (inherit samtools) + (version "0.1.19") + (source + (origin + (method url-fetch) + (uri + (string-append "mirror://sourceforge/samtools/" + version "/samtools-" version ".tar.bz2")) + (sha256 + (base32 "1m33xsfwz0s8qi45lylagfllqg7fphf4dr0780rsvw75av9wk06h")))) + (arguments + (substitute-keyword-arguments (package-arguments samtools) + ((#:tests? tests) #f) ;no "check" target + ((#:phases phases) + `(modify-phases ,phases + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append + (assoc-ref outputs "out") "/bin"))) + (mkdir-p bin) + (copy-file "samtools" + (string-append bin "/samtools"))))) + (delete 'patch-tests))))))) + +(define-public ngs-sdk + (package + (name "ngs-sdk") + (version "1.1.0") + (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 + "09fakv9w87lfg9g70kwzmnryqdjj1sz2c7kw01i6drjf787gkjhw")))) + (build-system gnu-build-system) + (arguments + `(#:parallel-build? #f ; not supported + #:tests? #f ; no "check" target + #:phases + (alist-replace + 'configure + (lambda* (#:key 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 46d4509fa8 (no release yet). + (substitute* "setup/konfigure.perl" + (((string-append "\\$\\(subst " + "(\\$\\(VERSION[^\\)]*\\))," + "(\\$\\([^\\)]+\\))," + "(\\$\\([^\\)]+\\)|\\$\\@)" + "\\)") + _ pattern replacement target) + (string-append "$(patsubst " + "%" pattern "," + "%" replacement "," + target ")"))) + + ;; The 'configure' script doesn't recognize things like + ;; '--enable-fast-install'. + (zero? (system* "./configure" + (string-append "--build-prefix=" (getcwd) "/build") + (string-append "--prefix=" out))))) + (alist-cons-after + 'unpack 'enter-dir + (lambda _ (chdir "ngs-sdk") #t) + %standard-phases)))) + (native-inputs `(("perl" ,perl))) + (home-page "https://github.com/ncbi/ngs") + (synopsis "API for accessing Next Generation Sequencing data") + (description + "NGS is a domain-specific API for accessing reads, alignments and pileups +produced from Next Generation Sequencing. The API itself is independent from +any particular back-end implementation, and supports use of multiple back-ends +simultaneously.") + (license license:public-domain))) + +(define-public ngs-java + (package (inherit ngs-sdk) + (name "ngs-java") + (arguments + `(,@(substitute-keyword-arguments + `(#:modules ((guix build gnu-build-system) + (guix build utils) + (srfi srfi-1) + (srfi srfi-26)) + ,@(package-arguments ngs-sdk)) + ((#:phases phases) + `(alist-cons-after + 'enter-dir 'fix-java-symlink-installation + (lambda _ + ;; Only replace the version suffix, not the version number in + ;; the directory name. Reported here: + ;; https://github.com/ncbi/ngs/pull/4 + (substitute* "Makefile.java" + (((string-append "\\$\\(subst " + "(\\$\\(VERSION[^\\)]*\\))," + "(\\$\\([^\\)]+\\))," + "(\\$\\([^\\)]+\\)|\\$\\@)" + "\\)") + _ pattern replacement target) + (string-append "$(patsubst " + "%" pattern "," + "%" replacement "," + target ")")))) + (alist-replace + 'enter-dir (lambda _ (chdir "ngs-java") #t) + ,phases)))))) + (inputs + `(("jdk" ,icedtea6 "jdk") + ("ngs-sdk" ,ngs-sdk))) + (synopsis "Java bindings for NGS SDK"))) + +(define-public ncbi-vdb + (package + (name "ncbi-vdb") + (version "2.4.5-5") + (source + (origin + (method url-fetch) + (uri + (string-append "https://github.com/ncbi/ncbi-vdb/archive/" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1cj8nk6if8sqagv20vx36v566fdvhcaadf0x1ycnbgql6chbs6vy")))) + (build-system gnu-build-system) + (arguments + `(#:parallel-build? #f ; not supported + #:tests? #f ; no "check" target + #:phases + (alist-replace + 'configure + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + ;; Only replace the version suffix, not the version number in the + ;; directory name; fixed in commit 4dbba5c6a809 (no release yet). + (substitute* "setup/konfigure.perl" + (((string-append "\\$\\(subst " + "(\\$\\(VERSION[^\\)]*\\))," + "(\\$\\([^\\)]+\\))," + "(\\$\\([^\\)]+\\)|\\$\\@)" + "\\)") + _ pattern replacement target) + (string-append "$(patsubst " + "%" pattern "," + "%" replacement "," + target ")"))) + + ;; Override include path for libmagic + (substitute* "setup/package.prl" + (("name => 'magic', Include => '/usr/include'") + (string-append "name=> 'magic', Include => '" + (assoc-ref inputs "libmagic") + "/include" "'"))) + + ;; Install kdf5 library (needed by sra-tools) + (substitute* "build/Makefile.install" + (("LIBRARIES_TO_INSTALL =") + "LIBRARIES_TO_INSTALL = kdf5.$(VERSION_LIBX) kdf5.$(VERSION_SHLX)")) + + ;; The 'configure' script doesn't recognize things like + ;; '--enable-fast-install'. + (zero? (system* + "./configure" + (string-append "--build-prefix=" (getcwd) "/build") + (string-append "--prefix=" (assoc-ref outputs "out")) + (string-append "--debug") + (string-append "--with-xml2-prefix=" + (assoc-ref inputs "libxml2")) + (string-append "--with-ngs-sdk-prefix=" + (assoc-ref inputs "ngs-sdk")) + (string-append "--with-ngs-java-prefix=" + (assoc-ref inputs "ngs-java")) + (string-append "--with-hdf5-prefix=" + (assoc-ref inputs "hdf5")))))) + (alist-cons-after + 'install 'install-interfaces + (lambda* (#:key system outputs #:allow-other-keys) + ;; Install interface libraries + (mkdir (string-append (assoc-ref outputs "out") "/ilib")) + (copy-recursively (string-append "build/ncbi-vdb/linux/gcc/" + (car (string-split system #\-)) + "/rel/ilib") + (string-append (assoc-ref outputs "out") + "/ilib")) + ;; Install interface headers + (copy-recursively "interfaces" + (string-append (assoc-ref outputs "out") + "/include"))) + %standard-phases)))) + (inputs + `(("libxml2" ,libxml2) + ("ngs-sdk" ,ngs-sdk) + ("ngs-java" ,ngs-java) + ("libmagic" ,file) + ("hdf5" ,hdf5))) + (native-inputs `(("perl" ,perl))) + (home-page "https://github.com/ncbi/ncbi-vdb") + (synopsis "Database engine for genetic information") + (description + "The NCBI-VDB library implements a highly compressed columnar data +warehousing engine that is most often used to store genetic information. +Databases are stored in a portable image within the file system, and can be +accessed/downloaded on demand across HTTP.") + (license license:public-domain))) + +(define-public sra-tools + (package + (name "sra-tools") + (version "2.4.5-5") + (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")) + (sha256 + (base32 + "11nrnvz7a012f4iryf0wiwrid0h111grsfxbxa9j51h3f2xbvgns")))) + (build-system gnu-build-system) + (arguments + `(#:parallel-build? #f ; not supported + #:tests? #f ; no "check" target + #:phases + (alist-replace + 'configure + (lambda* (#:key inputs outputs #:allow-other-keys) + ;; The build system expects a directory containing the sources and + ;; raw build output of ncbi-vdb, including files that are not + ;; installed. Since we are building against an installed version of + ;; ncbi-vdb, the following modifications are needed. + (substitute* "setup/konfigure.perl" + ;; Make the configure script look for the "ilib" directory of + ;; "ncbi-vdb" without first checking for the existence of a + ;; matching library in its "lib" directory. + (("^ my \\$f = File::Spec->catdir\\(\\$libdir, \\$lib\\);") + "my $f = File::Spec->catdir($ilibdir, $ilib);") + ;; Look for interface libraries in ncbi-vdb's "ilib" directory. + (("my \\$ilibdir = File::Spec->catdir\\(\\$builddir, 'ilib'\\);") + "my $ilibdir = File::Spec->catdir($dir, 'ilib');")) + + ;; The 'configure' script doesn't recognize things like + ;; '--enable-fast-install'. + (zero? (system* + "./configure" + (string-append "--build-prefix=" (getcwd) "/build") + (string-append "--prefix=" (assoc-ref outputs "out")) + (string-append "--debug") + (string-append "--with-fuse-prefix=" + (assoc-ref inputs "fuse")) + (string-append "--with-magic-prefix=" + (assoc-ref inputs "libmagic")) + ;; TODO: building with libxml2 fails with linker errors + ;; (string-append "--with-xml2-prefix=" + ;; (assoc-ref inputs "libxml2")) + (string-append "--with-ncbi-vdb-sources=" + (assoc-ref inputs "ncbi-vdb")) + (string-append "--with-ncbi-vdb-build=" + (assoc-ref inputs "ncbi-vdb")) + (string-append "--with-ngs-sdk-prefix=" + (assoc-ref inputs "ngs-sdk")) + (string-append "--with-hdf5-prefix=" + (assoc-ref inputs "hdf5"))))) + %standard-phases))) + (native-inputs `(("perl" ,perl))) + (inputs + `(("ngs-sdk" ,ngs-sdk) + ("ncbi-vdb" ,ncbi-vdb) + ("libmagic" ,file) + ("fuse" ,fuse) + ("hdf5" ,hdf5) + ("zlib" ,zlib))) + (home-page "http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software") + (synopsis "Tools and libraries for reading and writing sequencing data") + (description + "The SRA Toolkit from NCBI is a collection of tools and libraries for +reading of sequencing files from the Sequence Read Archive (SRA) database and +writing files into the .sra format.") + (license license:public-domain))) + (define-public seqan (package (name "seqan") @@ -810,3 +1575,188 @@ chimeric (fusion) transcripts, and is also capable of mapping full-length RNA sequences.") ;; STAR is licensed under GPLv3 or later; htslib is MIT-licensed. (license license:gpl3+))) + +(define-public subread + (package + (name "subread") + (version "1.4.6-p2") + (source (origin + (method url-fetch) + (uri (string-append + "mirror://sourceforge/subread/subread-" + version "-source.tar.gz")) + (sha256 + (base32 + "06sv9mpcsdj6p68y15d6gi70lca3lxmzk0dn61hg0kfsa7rxmsr3")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ;no "check" target + #:make-flags '("-f" "Makefile.Linux") + #:phases + (alist-cons-after + 'unpack 'enter-dir + (lambda _ (chdir "src") #t) + (alist-replace + 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) + (mkdir-p bin) + (copy-recursively "../bin" bin))) + ;; no "configure" script + (alist-delete 'configure %standard-phases))))) + (inputs `(("zlib" ,zlib))) + (home-page "http://bioinf.wehi.edu.au/subread-package/") + (synopsis "Tool kit for processing next-gen sequencing data") + (description + "The subread package contains the following tools: subread aligner, a +general-purpose read aligner; subjunc aligner: detecting exon-exon junctions +and mapping RNA-seq reads; featureCounts: counting mapped reads for genomic +features; exactSNP: a SNP caller that discovers SNPs by testing signals +against local background noises.") + (license license:gpl3+))) + +(define-public shogun + (package + (name "shogun") + (version "4.0.0") + (source + (origin + (method url-fetch) + (uri (string-append + "ftp://shogun-toolbox.org/shogun/releases/" + (version-major+minor version) + "/sources/shogun-" version ".tar.bz2")) + (sha256 + (base32 + "159nlijnb7mnrv9za80wnm1shwvy45hgrqzn51hxy7gw4z6d6fdb")))) + (build-system cmake-build-system) + (arguments + '(#:tests? #f ;no check target + #:phases + (alist-cons-after + 'unpack 'delete-broken-symlinks + (lambda _ + (for-each delete-file '("applications/arts/data" + "applications/asp/data" + "applications/easysvm/data" + "applications/msplicer/data" + "applications/ocr/data" + "examples/documented/data" + "examples/documented/matlab_static" + "examples/documented/octave_static" + "examples/undocumented/data" + "examples/undocumented/matlab_static" + "examples/undocumented/octave_static" + "tests/integration/data" + "tests/integration/matlab_static" + "tests/integration/octave_static" + "tests/integration/python_modular/tests")) + #t) + (alist-cons-after + 'unpack 'change-R-target-path + (lambda* (#:key outputs #:allow-other-keys) + (substitute* '("src/interfaces/r_modular/CMakeLists.txt" + "src/interfaces/r_static/CMakeLists.txt" + "examples/undocumented/r_modular/CMakeLists.txt") + (("\\$\\{R_COMPONENT_LIB_PATH\\}") + (string-append (assoc-ref outputs "out") + "/lib/R/library/"))) + #t) + (alist-cons-after + 'unpack 'fix-octave-modules + (lambda* (#:key outputs #:allow-other-keys) + (substitute* '("src/interfaces/octave_modular/CMakeLists.txt" + "src/interfaces/octave_static/CMakeLists.txt") + (("^include_directories\\(\\$\\{OCTAVE_INCLUDE_DIRS\\}") + "include_directories(${OCTAVE_INCLUDE_DIRS} ${OCTAVE_INCLUDE_DIRS}/octave")) + + ;; change target directory + (substitute* "src/interfaces/octave_modular/CMakeLists.txt" + (("\\$\\{OCTAVE_OCT_LOCAL_API_FILE_DIR\\}") + (string-append (assoc-ref outputs "out") + "/share/octave/packages"))) + #t) + (alist-cons-before + 'build 'set-HOME + ;; $HOME needs to be set at some point during the build phase + (lambda _ (setenv "HOME" "/tmp") #t) + %standard-phases)))) + #:configure-flags + (list "-DUSE_SVMLIGHT=OFF" ;disable proprietary SVMLIGHT + ;;"-DJavaModular=ON" ;requires unpackaged jblas + ;;"-DRubyModular=ON" ;requires unpackaged ruby-narray + ;;"-DPerlModular=ON" ;"FindPerlLibs" does not exist + ;;"-DLuaModular=ON" ;fails because lua doesn't build pkgconfig file + "-DOctaveModular=ON" + "-DOctaveStatic=ON" + "-DPythonModular=ON" + "-DPythonStatic=ON" + "-DRModular=ON" + "-DRStatic=ON" + "-DCmdLineStatic=ON"))) + (inputs + `(("python" ,python) + ("numpy" ,python-numpy) + ("r" ,r) + ("octave" ,octave) + ("swig" ,swig) + ("hdf5" ,hdf5) + ("atlas" ,atlas) + ("arpack" ,arpack-ng) + ("lapack" ,lapack) + ("glpk" ,glpk) + ("libxml2" ,libxml2) + ("lzo" ,lzo) + ("zlib" ,zlib))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (home-page "http://shogun-toolbox.org/") + (synopsis "Machine learning toolbox") + (description + "The Shogun Machine learning toolbox provides a wide range of unified and +efficient Machine Learning (ML) methods. The toolbox seamlessly allows to +combine multiple data representations, algorithm classes, and general purpose +tools. This enables both rapid prototyping of data pipelines and extensibility +in terms of new algorithms.") + (license license:gpl3+))) + +(define-public vcftools + (package + (name "vcftools") + (version "0.1.12b") + (source (origin + (method url-fetch) + (uri (string-append + "mirror://sourceforge/vcftools/vcftools_" + version ".tar.gz")) + (sha256 + (base32 + "148al9h7f8g8my2qdnpax51kdd2yjrivlx6frvakf4lz5r8j88wx")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; no "check" target + #:make-flags (list + "CFLAGS=-O2" ; override "-m64" flag + (string-append "PREFIX=" (assoc-ref %outputs "out")) + (string-append "MANDIR=" (assoc-ref %outputs "out") + "/share/man/man1")) + #:phases + (alist-cons-after + 'unpack 'patch-manpage-install + (lambda _ + (substitute* "Makefile" + (("cp \\$\\{PREFIX\\}/cpp/vcftools.1") "cp ./cpp/vcftools.1"))) + (alist-delete 'configure %standard-phases)))) + (inputs + `(("perl" ,perl) + ("zlib" ,zlib))) + (home-page "http://vcftools.sourceforge.net/") + (synopsis "Tools for working with VCF files") + (description + "VCFtools is a program package designed for working with VCF files, such +as those generated by the 1000 Genomes Project. The aim of VCFtools is to +provide easily accessible methods for working with complex genetic variation +data in the form of VCF files.") + ;; The license is declared as LGPLv3 in the README and + ;; at http://vcftools.sourceforge.net/license.html + (license license:lgpl3))) |