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15/17: gnu: Add java-htsjdk-2.10.1.
From: |
Ricardo Wurmus |
Subject: |
15/17: gnu: Add java-htsjdk-2.10.1. |
Date: |
Sat, 3 Mar 2018 15:28:38 -0500 (EST) |
rekado pushed a commit to branch master
in repository guix.
commit 719fa958f395a44c87377eb61a6f81a7a57603fe
Author: Ricardo Wurmus <address@hidden>
Date: Thu Mar 1 19:41:47 2018 +0100
gnu: Add java-htsjdk-2.10.1.
* gnu/packages/bioinformatics.scm (java-htsjdk-2.10.1): New variable.
---
gnu/packages/bioinformatics.scm | 27 +++++++++++++++++++++++++++
1 file changed, 27 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 5056726..09a64a8 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
- 09/17: gnu: Add java-biojava-phylo., (continued)
- 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, 2018/03/03
- 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
- 10/17: gnu: Add java-biojava-alignment., Ricardo Wurmus, 2018/03/03
- 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 <=
- 17/17: gnu: Add dropseq-tools., Ricardo Wurmus, 2018/03/03