gnu: Add SEEK.
* gnu/packages/bioinformatics.scm (seek): New variable.
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@ -27,6 +27,7 @@
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#:use-module (guix utils)
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#:use-module (guix download)
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#:use-module (guix git-download)
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#:use-module (guix hg-download)
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#:use-module (guix build-system ant)
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#:use-module (guix build-system gnu)
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#:use-module (guix build-system cmake)
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@ -51,6 +52,7 @@
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#:use-module (gnu packages gcc)
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#:use-module (gnu packages java)
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#:use-module (gnu packages linux)
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#:use-module (gnu packages logging)
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#:use-module (gnu packages machine-learning)
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#:use-module (gnu packages maths)
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#:use-module (gnu packages mpi)
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@ -61,6 +63,7 @@
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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 readline)
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#:use-module (gnu packages ruby)
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#:use-module (gnu packages statistics)
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#:use-module (gnu packages tbb)
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@ -3000,6 +3003,75 @@ while RNA-seq specific modules evaluate sequencing saturation, mapped reads
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distribution, coverage uniformity, strand specificity, etc.")
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(license license:gpl3+)))
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(define-public seek
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;; There are no release tarballs. According to the installation
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;; instructions at http://seek.princeton.edu/installation.jsp, the latest
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;; stable release is identified by this changeset ID.
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(let ((changeset "2329130")
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(revision "1"))
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(package
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(name "seek")
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(version (string-append "0-" revision "." changeset))
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(source (origin
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(method hg-fetch)
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(uri (hg-reference
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(url "https://bitbucket.org/libsleipnir/sleipnir")
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(changeset changeset)))
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(sha256
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(base32
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"0qrvilwh18dpbhkf92qvxbmay0j75ra3jg2wrhz67gf538zzphsx"))))
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(build-system gnu-build-system)
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(arguments
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`(#:modules ((srfi srfi-1)
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(guix build gnu-build-system)
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(guix build utils))
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#:phases
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(let ((dirs '("SeekMiner"
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"SeekEvaluator"
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"SeekPrep"
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"Distancer"
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"Data2DB"
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"PCL2Bin")))
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(modify-phases %standard-phases
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(add-before 'configure 'bootstrap
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(lambda _
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(zero? (system* "bash" "gen_auto"))))
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(add-after 'build 'build-additional-tools
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(lambda* (#:key make-flags #:allow-other-keys)
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(every (lambda (dir)
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(with-directory-excursion (string-append "tools/" dir)
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(zero? (apply system* "make" make-flags))))
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dirs)))
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(add-after 'install 'install-additional-tools
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(lambda* (#:key make-flags #:allow-other-keys)
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(fold (lambda (dir result)
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(with-directory-excursion (string-append "tools/" dir)
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(and result
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(zero? (apply system*
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`("make" ,@make-flags "install"))))))
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#t dirs)))))))
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(inputs
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`(("gsl" ,gsl)
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("boost" ,boost)
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("libsvm" ,libsvm)
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("readline" ,readline)
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("gengetopt" ,gengetopt)
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("log4cpp" ,log4cpp)))
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(native-inputs
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`(("autoconf" ,autoconf)
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("automake" ,automake)
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("perl" ,perl)))
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(home-page "http://seek.princeton.edu")
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(synopsis "Gene co-expression search engine")
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(description
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"SEEK is a computational gene co-expression search engine. SEEK provides
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biologists with a way to navigate the massive human expression compendium that
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now contains thousands of expression datasets. SEEK returns a robust ranking
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of co-expressed genes in the biological area of interest defined by the user's
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query genes. It also prioritizes thousands of expression datasets according
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to the user's query of interest.")
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(license license:cc-by3.0))))
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(define-public samtools
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(package
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(name "samtools")
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