gnu: Add dropseq-tools.
* gnu/packages/bioinformatics.scm (dropseq-tools): New variable.master
Ricardo Wurmus
Ricardo Wurmus
parent
72299db9fe
commit
1adeef3194
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@ -12504,3 +12504,140 @@ contains
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@item reading and writing of popular alignment file formats;
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@item a single-, or multi- threaded multiple sequence alignment algorithm.
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@end itemize\n")))
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(define-public dropseq-tools
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(package
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(name "dropseq-tools")
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(version "1.13")
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(source
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(origin
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(method url-fetch)
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(uri "http://mccarrolllab.com/download/1276/")
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(file-name (string-append "dropseq-tools-" version ".zip"))
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(sha256
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(base32
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"0yrffckxqk5l8b5xb6z4laq157zd9mdypr2p4b4vq2bhjzi1sj0s"))
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;; Delete bundled libraries
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(modules '((guix build utils)))
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(snippet
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'(begin
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(for-each delete-file (find-files "jar/lib" "\\.jar$"))
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(delete-file-recursively "3rdParty")))))
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(build-system ant-build-system)
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(arguments
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`(#:tests? #f ; test data are not included
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#:test-target "test"
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#:build-target "all"
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#:source-dir "public/src/"
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#:jdk ,icedtea-8
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#:make-flags
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(list (string-append "-Dpicard.executable.dir="
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(assoc-ref %build-inputs "java-picard")
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"/share/java/"))
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#:modules ((ice-9 match)
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(srfi srfi-1)
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(guix build utils)
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(guix build java-utils)
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(guix build ant-build-system))
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#:phases
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(modify-phases %standard-phases
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;; All dependencies must be linked to "lib", because that's where
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;; they will be searched for when the Class-Path property of the
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;; manifest is computed.
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(add-after 'unpack 'record-references
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(lambda* (#:key inputs #:allow-other-keys)
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(mkdir-p "jar/lib")
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(let ((dirs (filter-map (match-lambda
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((name . dir)
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(if (and (string-prefix? "java-" name)
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(not (string=? name "java-testng")))
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dir #f)))
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inputs)))
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(for-each (lambda (jar)
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(symlink jar (string-append "jar/lib/" (basename jar))))
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(append-map (lambda (dir) (find-files dir "\\.jar$"))
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dirs)))
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#t))
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;; There is no installation target
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(replace 'install
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(lambda* (#:key inputs outputs #:allow-other-keys)
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(let* ((out (assoc-ref outputs "out"))
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(bin (string-append out "/bin"))
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(share (string-append out "/share/java/"))
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(lib (string-append share "/lib/"))
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(scripts (list "BAMTagHistogram"
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"BAMTagofTagCounts"
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"BaseDistributionAtReadPosition"
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"CollapseBarcodesInPlace"
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"CollapseTagWithContext"
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"ConvertToRefFlat"
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"CreateIntervalsFiles"
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"DetectBeadSynthesisErrors"
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"DigitalExpression"
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"Drop-seq_alignment.sh"
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"FilterBAM"
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"FilterBAMByTag"
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"GatherGeneGCLength"
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"GatherMolecularBarcodeDistributionByGene"
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"GatherReadQualityMetrics"
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"PolyATrimmer"
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"ReduceGTF"
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"SelectCellsByNumTranscripts"
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"SingleCellRnaSeqMetricsCollector"
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"TagBamWithReadSequenceExtended"
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"TagReadWithGeneExon"
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"TagReadWithInterval"
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"TrimStartingSequence"
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"ValidateReference")))
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(for-each mkdir-p (list bin share lib))
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(install-file "dist/dropseq.jar" share)
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(for-each (lambda (script)
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(chmod script #o555)
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(install-file script bin))
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scripts)
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(substitute* (map (lambda (script)
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(string-append bin "/" script))
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scripts)
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(("^java") (which "java"))
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(("jar_deploy_dir=.*")
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(string-append "jar_deploy_dir=" share "\n"))))
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#t))
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;; FIXME: We do this after stripping jars because we don't want it to
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;; copy all these jars and strip them. We only want to install
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;; links. Arguably, this is a problem with the ant-build-system.
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(add-after 'strip-jar-timestamps 'install-links
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(lambda* (#:key outputs #:allow-other-keys)
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(let* ((out (assoc-ref outputs "out"))
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(share (string-append out "/share/java/"))
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(lib (string-append share "/lib/")))
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(for-each (lambda (jar)
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(symlink (readlink jar)
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(string-append lib (basename jar))))
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(find-files "jar/lib" "\\.jar$")))
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#t)))))
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(inputs
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`(("jdk" ,icedtea-8)
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("java-picard" ,java-picard-2.10.3)
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("java-log4j-1.2-api" ,java-log4j-1.2-api)
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("java-commons-math3" ,java-commons-math3)
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("java-commons-jexl2" ,java-commons-jexl-2)
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("java-commons-collections4" ,java-commons-collections4)
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("java-commons-lang2" ,java-commons-lang)
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("java-commons-io" ,java-commons-io)
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("java-snappy-1.0.3-rc3" ,java-snappy-1)
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("java-guava" ,java-guava)
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("java-la4j" ,java-la4j)
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("java-biojava-core" ,java-biojava-core-4.0)
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("java-biojava-alignment" ,java-biojava-alignment-4.0)
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("java-jdistlib" ,java-jdistlib)
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("java-simple-xml" ,java-simple-xml)
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("java-snakeyaml" ,java-snakeyaml)))
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(native-inputs
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`(("unzip" ,unzip)
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("java-testng" ,java-testng)))
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(home-page "http://mccarrolllab.com/dropseq/")
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(synopsis "Tools for Drop-seq analyses")
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(description "Drop-seq is a technology to enable biologists to
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analyze RNA expression genome-wide in thousands of individual cells at
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once. This package provides tools to perform Drop-seq analyses.")
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(license license:expat)))
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