gnu: Add eXpress.
* gnu/packages/bioinformatics.scm (express): New variable.
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@ -28,6 +28,7 @@
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#:use-module (guix build-system trivial)
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#:use-module (guix build-system trivial)
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#:use-module (gnu packages)
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#:use-module (gnu packages)
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#:use-module (gnu packages base)
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#:use-module (gnu packages base)
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#:use-module (gnu packages boost)
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#:use-module (gnu packages compression)
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#:use-module (gnu packages compression)
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#:use-module (gnu packages file)
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#:use-module (gnu packages file)
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#:use-module (gnu packages java)
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#:use-module (gnu packages java)
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@ -37,6 +38,7 @@
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#:use-module (gnu packages perl)
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#:use-module (gnu packages perl)
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#:use-module (gnu packages pkg-config)
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#:use-module (gnu packages pkg-config)
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#:use-module (gnu packages popt)
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#:use-module (gnu packages popt)
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#:use-module (gnu packages protobuf)
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#:use-module (gnu packages python)
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#:use-module (gnu packages python)
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#:use-module (gnu packages statistics)
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#:use-module (gnu packages statistics)
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#:use-module (gnu packages swig)
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#:use-module (gnu packages swig)
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@ -530,6 +532,51 @@ file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.")
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other types of unwanted sequence from high-throughput sequencing reads.")
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other types of unwanted sequence from high-throughput sequencing reads.")
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(license license:expat)))
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(license license:expat)))
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(define-public express
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(package
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(name "express")
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(version "1.5.1")
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(source (origin
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(method url-fetch)
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(uri
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(string-append
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"http://bio.math.berkeley.edu/eXpress/downloads/express-"
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version "/express-" version "-src.tgz"))
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(sha256
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(base32
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"03rczxd0gjp2l1jxcmjfmf5j94j77zqyxa6x063zsc585nj40n0c"))))
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(build-system cmake-build-system)
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(arguments
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`(#:tests? #f ;no "check" target
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#:phases
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(alist-cons-after
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'unpack 'use-shared-boost-libs-and-set-bamtools-paths
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(lambda* (#:key inputs #:allow-other-keys)
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(substitute* "CMakeLists.txt"
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(("set\\(Boost_USE_STATIC_LIBS ON\\)")
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"set(Boost_USE_STATIC_LIBS OFF)")
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(("\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/bamtools/include")
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(string-append (assoc-ref inputs "bamtools") "/include/bamtools")))
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(substitute* "src/CMakeLists.txt"
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(("\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/\\.\\./bamtools/lib")
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(string-append (assoc-ref inputs "bamtools") "/lib/bamtools")))
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#t)
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%standard-phases)))
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(inputs
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`(("boost" ,boost)
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("bamtools" ,bamtools)
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("protobuf" ,protobuf)
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("zlib" ,zlib)))
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(home-page "http://bio.math.berkeley.edu/eXpress")
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(synopsis "Streaming quantification for high-throughput genomic sequencing")
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(description
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"eXpress is a streaming tool for quantifying the abundances of a set of
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target sequences from sampled subsequences. Example applications include
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transcript-level RNA-Seq quantification, allele-specific/haplotype expression
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analysis (from RNA-Seq), transcription factor binding quantification in
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ChIP-Seq, and analysis of metagenomic data.")
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(license license:artistic2.0)))
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(define-public fastx-toolkit
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(define-public fastx-toolkit
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(package
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(package
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(name "fastx-toolkit")
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(name "fastx-toolkit")
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