diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 109 |
1 files changed, 109 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4fd9459350..ccfda627f3 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -28,6 +28,7 @@ #: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) @@ -37,6 +38,7 @@ #: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) @@ -46,6 +48,29 @@ #: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 + (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") @@ -507,6 +532,51 @@ file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.") 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") @@ -1386,6 +1456,45 @@ 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") |