diff options
| author | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2018-03-01 19:41:46 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2018-03-03 21:27:57 +0100 |
| commit | 9a599c17b7dfca56ff8290902057ee6da933aed2 (patch) | |
| tree | 02519cac5ddaa6bdabf7b07c88e98c3df6704dee /gnu/packages | |
| parent | 9ac7db1830a1b324524aa7d383c5f1b5e348237f (diff) | |
gnu: Add java-htsjdk-latest.
* gnu/packages/bioinformatics.scm (java-htsjdk-latest): New variable.
Diffstat (limited to 'gnu/packages')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 43 |
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 |