gnu: Add java-picard-2.10.3.
* gnu/packages/bioinformatics.scm (java-picard-2.10.3): New variable.
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@ -3151,6 +3151,90 @@ commonly used for high-throughput sequencing data such as SAM, BAM, CRAM and
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VCF.")
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VCF.")
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(license license:expat)))
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(license license:expat)))
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;; This is needed for dropseq-tools
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(define-public java-picard-2.10.3
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(package
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(name "java-picard")
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(version "2.10.3")
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(source (origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/broadinstitute/picard.git")
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(commit version)))
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(file-name (string-append "java-picard-" version "-checkout"))
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(sha256
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(base32
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"1ajlx31l6i1k3y2rhnmgq07sz99g2czqfqgkr9mihmdjp3gwjhvi"))))
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(build-system ant-build-system)
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(arguments
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`(#:jar-name "picard.jar"
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;; Tests require jacoco:coverage.
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#:tests? #f
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#:jdk ,icedtea-8
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#:main-class "picard.cmdline.PicardCommandLine"
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#:modules ((guix build ant-build-system)
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(guix build utils)
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(guix build java-utils)
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(sxml simple)
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(sxml transform)
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(sxml xpath))
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#:phases
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(modify-phases %standard-phases
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(add-after 'unpack 'remove-useless-build.xml
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(lambda _ (delete-file "build.xml") #t))
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;; This is necessary to ensure that htsjdk is found when using
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;; picard.jar as an executable.
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(add-before 'build 'edit-classpath-in-manifest
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(lambda* (#:key inputs #:allow-other-keys)
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(chmod "build.xml" #o664)
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(call-with-output-file "build.xml.new"
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(lambda (port)
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(sxml->xml
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(pre-post-order
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(with-input-from-file "build.xml"
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(lambda _ (xml->sxml #:trim-whitespace? #t)))
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`((target . ,(lambda (tag . kids)
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(let ((name ((sxpath '(name *text*))
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(car kids)))
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;; FIXME: We're breaking the line
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;; early with a dummy path to
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;; ensure that the store reference
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;; isn't broken apart and can still
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;; be found by the reference
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;; scanner.
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(msg (format #f
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"\
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Class-Path: /~a \
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~a/share/java/htsjdk.jar${line.separator}"
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;; maximum line length is 70
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(string-tabulate (const #\b) 57)
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(assoc-ref inputs "java-htsjdk"))))
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(if (member "manifest" name)
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`(,tag ,@kids
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(echo
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(@ (message ,msg)
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(file "${manifest.file}")
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(append "true"))))
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`(,tag ,@kids)))))
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(*default* . ,(lambda (tag . kids) `(,tag ,@kids)))
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(*text* . ,(lambda (_ txt) txt))))
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port)))
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(rename-file "build.xml.new" "build.xml")
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#t)))))
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(propagated-inputs
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`(("java-htsjdk" ,java-htsjdk-2.10.1)))
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(native-inputs
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`(("java-testng" ,java-testng)
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("java-guava" ,java-guava)))
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(home-page "http://broadinstitute.github.io/picard/")
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(synopsis "Tools for manipulating high-throughput sequencing data and formats")
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(description "Picard is a set of Java command line tools for manipulating
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high-throughput sequencing (HTS) data and formats. Picard is implemented
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using the HTSJDK Java library to support accessing file formats that are
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commonly used for high-throughput sequencing data such as SAM, BAM, CRAM and
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VCF.")
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(license license:expat)))
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;; This is the last version of Picard to provide net.sf.samtools
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;; This is the last version of Picard to provide net.sf.samtools
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(define-public java-picard-1.113
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(define-public java-picard-1.113
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(package (inherit java-picard)
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(package (inherit java-picard)
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