gnu: Add java-picard-2.10.3.

* gnu/packages/bioinformatics.scm (java-picard-2.10.3): New variable.
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Ricardo Wurmus 2018-03-01 19:41:48 +01:00 committed by Ricardo Wurmus
parent 719fa958f3
commit 72299db9fe
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@ -3151,6 +3151,90 @@ (define-public java-picard
VCF.") VCF.")
(license license:expat))) (license license:expat)))
;; This is needed for dropseq-tools
(define-public java-picard-2.10.3
(package
(name "java-picard")
(version "2.10.3")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/broadinstitute/picard.git")
(commit version)))
(file-name (string-append "java-picard-" version "-checkout"))
(sha256
(base32
"1ajlx31l6i1k3y2rhnmgq07sz99g2czqfqgkr9mihmdjp3gwjhvi"))))
(build-system ant-build-system)
(arguments
`(#:jar-name "picard.jar"
;; Tests require jacoco:coverage.
#:tests? #f
#:jdk ,icedtea-8
#:main-class "picard.cmdline.PicardCommandLine"
#:modules ((guix build ant-build-system)
(guix build utils)
(guix build java-utils)
(sxml simple)
(sxml transform)
(sxml xpath))
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'remove-useless-build.xml
(lambda _ (delete-file "build.xml") #t))
;; This is necessary to ensure that htsjdk is found when using
;; picard.jar as an executable.
(add-before 'build 'edit-classpath-in-manifest
(lambda* (#:key inputs #:allow-other-keys)
(chmod "build.xml" #o664)
(call-with-output-file "build.xml.new"
(lambda (port)
(sxml->xml
(pre-post-order
(with-input-from-file "build.xml"
(lambda _ (xml->sxml #:trim-whitespace? #t)))
`((target . ,(lambda (tag . kids)
(let ((name ((sxpath '(name *text*))
(car kids)))
;; FIXME: We're breaking the line
;; early with a dummy path to
;; ensure that the store reference
;; isn't broken apart and can still
;; be found by the reference
;; scanner.
(msg (format #f
"\
Class-Path: /~a \
~a/share/java/htsjdk.jar${line.separator}"
;; maximum line length is 70
(string-tabulate (const #\b) 57)
(assoc-ref inputs "java-htsjdk"))))
(if (member "manifest" name)
`(,tag ,@kids
(echo
(@ (message ,msg)
(file "${manifest.file}")
(append "true"))))
`(,tag ,@kids)))))
(*default* . ,(lambda (tag . kids) `(,tag ,@kids)))
(*text* . ,(lambda (_ txt) txt))))
port)))
(rename-file "build.xml.new" "build.xml")
#t)))))
(propagated-inputs
`(("java-htsjdk" ,java-htsjdk-2.10.1)))
(native-inputs
`(("java-testng" ,java-testng)
("java-guava" ,java-guava)))
(home-page "http://broadinstitute.github.io/picard/")
(synopsis "Tools for manipulating high-throughput sequencing data and formats")
(description "Picard is a set of Java command line tools for manipulating
high-throughput sequencing (HTS) data and formats. Picard is implemented
using the HTSJDK Java library to support accessing file formats that are
commonly used for high-throughput sequencing data such as SAM, BAM, CRAM and
VCF.")
(license license:expat)))
;; This is the last version of Picard to provide net.sf.samtools ;; This is the last version of Picard to provide net.sf.samtools
(define-public java-picard-1.113 (define-public java-picard-1.113
(package (inherit java-picard) (package (inherit java-picard)