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Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 137 |
1 files changed, 137 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 719f3e5f23..75468aa967 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12504,3 +12504,140 @@ contains @item reading and writing of popular alignment file formats; @item a single-, or multi- threaded multiple sequence alignment algorithm. @end itemize\n"))) + +(define-public dropseq-tools + (package + (name "dropseq-tools") + (version "1.13") + (source + (origin + (method url-fetch) + (uri "http://mccarrolllab.com/download/1276/") + (file-name (string-append "dropseq-tools-" version ".zip")) + (sha256 + (base32 + "0yrffckxqk5l8b5xb6z4laq157zd9mdypr2p4b4vq2bhjzi1sj0s")) + ;; Delete bundled libraries + (modules '((guix build utils))) + (snippet + '(begin + (for-each delete-file (find-files "jar/lib" "\\.jar$")) + (delete-file-recursively "3rdParty"))))) + (build-system ant-build-system) + (arguments + `(#:tests? #f ; test data are not included + #:test-target "test" + #:build-target "all" + #:source-dir "public/src/" + #:jdk ,icedtea-8 + #:make-flags + (list (string-append "-Dpicard.executable.dir=" + (assoc-ref %build-inputs "java-picard") + "/share/java/")) + #:modules ((ice-9 match) + (srfi srfi-1) + (guix build utils) + (guix build java-utils) + (guix build ant-build-system)) + #:phases + (modify-phases %standard-phases + ;; All dependencies must be linked to "lib", because that's where + ;; they will be searched for when the Class-Path property of the + ;; manifest is computed. + (add-after 'unpack 'record-references + (lambda* (#:key inputs #:allow-other-keys) + (mkdir-p "jar/lib") + (let ((dirs (filter-map (match-lambda + ((name . dir) + (if (and (string-prefix? "java-" name) + (not (string=? name "java-testng"))) + dir #f))) + inputs))) + (for-each (lambda (jar) + (symlink jar (string-append "jar/lib/" (basename jar)))) + (append-map (lambda (dir) (find-files dir "\\.jar$")) + dirs))) + #t)) + ;; There is no installation target + (replace 'install + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin")) + (share (string-append out "/share/java/")) + (lib (string-append share "/lib/")) + (scripts (list "BAMTagHistogram" + "BAMTagofTagCounts" + "BaseDistributionAtReadPosition" + "CollapseBarcodesInPlace" + "CollapseTagWithContext" + "ConvertToRefFlat" + "CreateIntervalsFiles" + "DetectBeadSynthesisErrors" + "DigitalExpression" + "Drop-seq_alignment.sh" + "FilterBAM" + "FilterBAMByTag" + "GatherGeneGCLength" + "GatherMolecularBarcodeDistributionByGene" + "GatherReadQualityMetrics" + "PolyATrimmer" + "ReduceGTF" + "SelectCellsByNumTranscripts" + "SingleCellRnaSeqMetricsCollector" + "TagBamWithReadSequenceExtended" + "TagReadWithGeneExon" + "TagReadWithInterval" + "TrimStartingSequence" + "ValidateReference"))) + (for-each mkdir-p (list bin share lib)) + (install-file "dist/dropseq.jar" share) + (for-each (lambda (script) + (chmod script #o555) + (install-file script bin)) + scripts) + (substitute* (map (lambda (script) + (string-append bin "/" script)) + scripts) + (("^java") (which "java")) + (("jar_deploy_dir=.*") + (string-append "jar_deploy_dir=" share "\n")))) + #t)) + ;; FIXME: We do this after stripping jars because we don't want it to + ;; copy all these jars and strip them. We only want to install + ;; links. Arguably, this is a problem with the ant-build-system. + (add-after 'strip-jar-timestamps 'install-links + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (share (string-append out "/share/java/")) + (lib (string-append share "/lib/"))) + (for-each (lambda (jar) + (symlink (readlink jar) + (string-append lib (basename jar)))) + (find-files "jar/lib" "\\.jar$"))) + #t))))) + (inputs + `(("jdk" ,icedtea-8) + ("java-picard" ,java-picard-2.10.3) + ("java-log4j-1.2-api" ,java-log4j-1.2-api) + ("java-commons-math3" ,java-commons-math3) + ("java-commons-jexl2" ,java-commons-jexl-2) + ("java-commons-collections4" ,java-commons-collections4) + ("java-commons-lang2" ,java-commons-lang) + ("java-commons-io" ,java-commons-io) + ("java-snappy-1.0.3-rc3" ,java-snappy-1) + ("java-guava" ,java-guava) + ("java-la4j" ,java-la4j) + ("java-biojava-core" ,java-biojava-core-4.0) + ("java-biojava-alignment" ,java-biojava-alignment-4.0) + ("java-jdistlib" ,java-jdistlib) + ("java-simple-xml" ,java-simple-xml) + ("java-snakeyaml" ,java-snakeyaml))) + (native-inputs + `(("unzip" ,unzip) + ("java-testng" ,java-testng))) + (home-page "http://mccarrolllab.com/dropseq/") + (synopsis "Tools for Drop-seq analyses") + (description "Drop-seq is a technology to enable biologists to +analyze RNA expression genome-wide in thousands of individual cells at +once. This package provides tools to perform Drop-seq analyses.") + (license license:expat))) |