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14/17: gnu: Add java-htsjdk-latest.
From: |
Ricardo Wurmus |
Subject: |
14/17: gnu: Add java-htsjdk-latest. |
Date: |
Sat, 3 Mar 2018 15:28:38 -0500 (EST) |
rekado pushed a commit to branch master
in repository guix.
commit 9a599c17b7dfca56ff8290902057ee6da933aed2
Author: Ricardo Wurmus <address@hidden>
Date: Thu Mar 1 19:41:46 2018 +0100
gnu: Add java-htsjdk-latest.
* gnu/packages/bioinformatics.scm (java-htsjdk-latest): New variable.
---
gnu/packages/bioinformatics.scm | 43 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 43 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index f44dc32..5056726 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
- branch master updated (bd97583 -> 1adeef3), Ricardo Wurmus, 2018/03/03
- 02/17: gnu: Add java-jlargearrays., Ricardo Wurmus, 2018/03/03
- 03/17: gnu: Add java-jtransforms., Ricardo Wurmus, 2018/03/03
- 05/17: gnu: Add java-biojava-core., Ricardo Wurmus, 2018/03/03
- 06/17: gnu: Add java-openchart2., Ricardo Wurmus, 2018/03/03
- 04/17: gnu: Add java-jdistlib., Ricardo Wurmus, 2018/03/03
- 09/17: gnu: Add java-biojava-phylo., Ricardo Wurmus, 2018/03/03
- 08/17: gnu: Add java-forester-1.005., Ricardo Wurmus, 2018/03/03
- 01/17: gnu: Add java-la4j., Ricardo Wurmus, 2018/03/03
- 14/17: gnu: Add java-htsjdk-latest.,
Ricardo Wurmus <=
- 07/17: gnu: Add java-forester., Ricardo Wurmus, 2018/03/03
- 11/17: gnu: Add java-biojava-core-4.0., Ricardo Wurmus, 2018/03/03
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- 12/17: gnu: Add java-biojava-phylo-4.0., Ricardo Wurmus, 2018/03/03
- 13/17: gnu: Add java-biojava-alignment-4.0., Ricardo Wurmus, 2018/03/03
- 16/17: gnu: Add java-picard-2.10.3., Ricardo Wurmus, 2018/03/03
- 15/17: gnu: Add java-htsjdk-2.10.1., Ricardo Wurmus, 2018/03/03
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