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authorRicardo Wurmus <ricardo.wurmus@mdc-berlin.de>2018-03-01 19:41:47 +0100
committerRicardo Wurmus <rekado@elephly.net>2018-03-03 21:27:59 +0100
commit719fa958f395a44c87377eb61a6f81a7a57603fe (patch)
tree3794007759f8eceed9d6abd07bb3acf1dcf28160 /gnu/packages/bioinformatics.scm
parent9a599c17b7dfca56ff8290902057ee6da933aed2 (diff)
downloadguix-719fa958f395a44c87377eb61a6f81a7a57603fe.tar
guix-719fa958f395a44c87377eb61a6f81a7a57603fe.tar.gz
gnu: Add java-htsjdk-2.10.1.
* gnu/packages/bioinformatics.scm (java-htsjdk-2.10.1): New variable.
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
-rw-r--r--gnu/packages/bioinformatics.scm27
1 files changed, 27 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 505672624d..09a64a8d4d 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3046,6 +3046,33 @@ sequencing (HTS) data. There are also an number of useful utilities for
manipulating HTS data.")
(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
;; recent version of java-htsjdk, which depends on gradle.
(define-public java-picard