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17/17: gnu: Add dropseq-tools.
From: |
Ricardo Wurmus |
Subject: |
17/17: gnu: Add dropseq-tools. |
Date: |
Sat, 3 Mar 2018 15:28:38 -0500 (EST) |
rekado pushed a commit to branch master
in repository guix.
commit 1adeef3194dd7c8da6e78b17fb33e71bb0c9e24f
Author: Ricardo Wurmus <address@hidden>
Date: Thu Mar 1 19:41:49 2018 +0100
gnu: Add dropseq-tools.
* gnu/packages/bioinformatics.scm (dropseq-tools): New variable.
---
gnu/packages/bioinformatics.scm | 137 ++++++++++++++++++++++++++++++++++++++++
1 file changed, 137 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 719f3e5..75468aa 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)))
- 08/17: gnu: Add java-forester-1.005., (continued)
- 08/17: gnu: Add java-forester-1.005., Ricardo Wurmus, 2018/03/03
- 01/17: gnu: Add java-la4j., Ricardo Wurmus, 2018/03/03
- 14/17: gnu: Add java-htsjdk-latest., Ricardo Wurmus, 2018/03/03
- 07/17: gnu: Add java-forester., Ricardo Wurmus, 2018/03/03
- 11/17: gnu: Add java-biojava-core-4.0., Ricardo Wurmus, 2018/03/03
- 10/17: gnu: Add java-biojava-alignment., Ricardo Wurmus, 2018/03/03
- 12/17: gnu: Add java-biojava-phylo-4.0., Ricardo Wurmus, 2018/03/03
- 13/17: gnu: Add java-biojava-alignment-4.0., Ricardo Wurmus, 2018/03/03
- 16/17: gnu: Add java-picard-2.10.3., Ricardo Wurmus, 2018/03/03
- 15/17: gnu: Add java-htsjdk-2.10.1., Ricardo Wurmus, 2018/03/03
- 17/17: gnu: Add dropseq-tools.,
Ricardo Wurmus <=