gnu: Add java-htsjdk-2.10.1.

* gnu/packages/bioinformatics.scm (java-htsjdk-2.10.1): New variable.
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Ricardo Wurmus 2018-03-01 19:41:47 +01:00 committed by Ricardo Wurmus
parent 9a599c17b7
commit 719fa958f3
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1 changed files with 27 additions and 0 deletions

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@ -3046,6 +3046,33 @@ sequencing (HTS) data. There are also an number of useful utilities for
manipulating HTS data.") manipulating HTS data.")
(license license:expat))) (license license:expat)))
;; This is needed for picard 2.10.3
(define-public java-htsjdk-2.10.1
(package (inherit java-htsjdk-latest)
(name "java-htsjdk")
(version "2.10.1")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/samtools/htsjdk.git")
(commit version)))
(file-name (string-append name "-" version "-checkout"))
(sha256
(base32
"1kxh7slm2pm3x9p6jxa1wqsq9a31dhiiflhxnxqcisan4k3rwia2"))))
(build-system ant-build-system)
(arguments
`(#:tests? #f ; tests require Scala
#:jdk ,icedtea-8
#:jar-name "htsjdk.jar"
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'remove-useless-build.xml
(lambda _ (delete-file "build.xml") #t))
;; The tests require the scalatest package.
(add-after 'unpack 'remove-tests
(lambda _ (delete-file-recursively "src/test") #t)))))))
;; This version matches java-htsjdk 2.3.0. Later versions also require a more ;; This version matches java-htsjdk 2.3.0. Later versions also require a more
;; recent version of java-htsjdk, which depends on gradle. ;; recent version of java-htsjdk, which depends on gradle.
(define-public java-picard (define-public java-picard