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gnu: Add java-htsjdk-latest.
* gnu/packages/bioinformatics.scm (java-htsjdk-latest): New variable.
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@ -3003,6 +3003,49 @@ (define-public java-htsjdk
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manipulating HTS data.")
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(license license:expat)))
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(define-public java-htsjdk-latest
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(package
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(name "java-htsjdk")
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(version "2.14.3")
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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/samtools/htsjdk.git")
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(commit version)))
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(file-name (string-append name "-" version "-checkout"))
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(sha256
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(base32
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"1lmya1fdjy03mz6zmdmd86j9v9vfhqb3952mqq075navx1i6g4bc"))))
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(build-system ant-build-system)
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(arguments
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`(#:tests? #f ; test require Scala
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#:jdk ,icedtea-8
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#:jar-name "htsjdk.jar"
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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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;; The tests require the scalatest package.
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(add-after 'unpack 'remove-tests
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(lambda _ (delete-file-recursively "src/test") #t)))))
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(inputs
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`(("java-ngs" ,java-ngs)
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("java-snappy-1" ,java-snappy-1)
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("java-commons-compress" ,java-commons-compress)
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("java-commons-logging-minimal" ,java-commons-logging-minimal)
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("java-commons-jexl-2" ,java-commons-jexl-2)
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("java-xz" ,java-xz)))
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(native-inputs
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`(("java-junit" ,java-junit)))
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(home-page "http://samtools.github.io/htsjdk/")
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(synopsis "Java API for high-throughput sequencing data (HTS) formats")
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(description
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"HTSJDK is an implementation of a unified Java library for accessing
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common file formats, such as SAM and VCF, used for high-throughput
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sequencing (HTS) data. There are also an number of useful utilities for
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manipulating HTS data.")
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(license license:expat)))
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;; This version matches java-htsjdk 2.3.0. Later versions also require a more
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;; recent version of java-htsjdk, which depends on gradle.
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(define-public java-picard
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