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authorRicardo Wurmus <ricardo.wurmus@mdc-berlin.de>2018-03-01 19:41:46 +0100
committerRicardo Wurmus <rekado@elephly.net>2018-03-03 21:27:57 +0100
commit9a599c17b7dfca56ff8290902057ee6da933aed2 (patch)
tree02519cac5ddaa6bdabf7b07c88e98c3df6704dee /gnu/packages/bioinformatics.scm
parent9ac7db1830a1b324524aa7d383c5f1b5e348237f (diff)
gnu: Add java-htsjdk-latest.
* gnu/packages/bioinformatics.scm (java-htsjdk-latest): New variable.
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
-rw-r--r--gnu/packages/bioinformatics.scm43
1 files changed, 43 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index f44dc32aa7..505672624d 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3003,6 +3003,49 @@ sequencing (HTS) data. There are also an number of useful utilities for
manipulating HTS data.")
(license license:expat)))
+(define-public java-htsjdk-latest
+ (package
+ (name "java-htsjdk")
+ (version "2.14.3")
+ (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
+ "1lmya1fdjy03mz6zmdmd86j9v9vfhqb3952mqq075navx1i6g4bc"))))
+ (build-system ant-build-system)
+ (arguments
+ `(#:tests? #f ; test 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)))))
+ (inputs
+ `(("java-ngs" ,java-ngs)
+ ("java-snappy-1" ,java-snappy-1)
+ ("java-commons-compress" ,java-commons-compress)
+ ("java-commons-logging-minimal" ,java-commons-logging-minimal)
+ ("java-commons-jexl-2" ,java-commons-jexl-2)
+ ("java-xz" ,java-xz)))
+ (native-inputs
+ `(("java-junit" ,java-junit)))
+ (home-page "http://samtools.github.io/htsjdk/")
+ (synopsis "Java API for high-throughput sequencing data (HTS) formats")
+ (description
+ "HTSJDK is an implementation of a unified Java library for accessing
+common file formats, such as SAM and VCF, used for high-throughput
+sequencing (HTS) data. There are also an number of useful utilities for
+manipulating HTS data.")
+ (license license:expat)))
+
;; This version matches java-htsjdk 2.3.0. Later versions also require a more
;; recent version of java-htsjdk, which depends on gradle.
(define-public java-picard