From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
To: 30666@debbugs.gnu.org
Cc: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Subject: [bug#30666] [PATCH 14/17] gnu: Add java-htsjdk-latest.
Date: Thu, 1 Mar 2018 19:41:46 +0100 [thread overview]
Message-ID: <20180301184149.27239-14-ricardo.wurmus@mdc-berlin.de> (raw)
In-Reply-To: <20180301184149.27239-1-ricardo.wurmus@mdc-berlin.de>
* 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 98c0aff3a..2402fa0e7 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3019,6 +3019,49 @@ 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
--
2.15.1
next prev parent reply other threads:[~2018-03-01 18:57 UTC|newest]
Thread overview: 19+ messages / expand[flat|nested] mbox.gz Atom feed top
2018-03-01 17:44 [bug#30666] [PATCH 00/17] Add dropseq-tools Ricardo Wurmus
2018-03-01 18:41 ` [bug#30666] [PATCH 01/17] gnu: Add java-la4j Ricardo Wurmus
2018-03-01 18:41 ` [bug#30666] [PATCH 02/17] gnu: Add java-jlargearrays Ricardo Wurmus
2018-03-01 18:41 ` [bug#30666] [PATCH 03/17] gnu: Add java-jtransforms Ricardo Wurmus
2018-03-01 18:41 ` [bug#30666] [PATCH 04/17] gnu: Add java-jdistlib Ricardo Wurmus
2018-03-01 18:41 ` [bug#30666] [PATCH 05/17] gnu: Add java-biojava-core Ricardo Wurmus
2018-03-01 18:41 ` [bug#30666] [PATCH 06/17] gnu: Add java-openchart2 Ricardo Wurmus
2018-03-01 18:41 ` [bug#30666] [PATCH 07/17] gnu: Add java-forester Ricardo Wurmus
2018-03-01 18:41 ` [bug#30666] [PATCH 08/17] gnu: Add java-forester-1.005 Ricardo Wurmus
2018-03-01 18:41 ` [bug#30666] [PATCH 09/17] gnu: Add java-biojava-phylo Ricardo Wurmus
2018-03-01 18:41 ` [bug#30666] [PATCH 10/17] gnu: Add java-biojava-alignment Ricardo Wurmus
2018-03-01 18:41 ` [bug#30666] [PATCH 11/17] gnu: Add java-biojava-core-4.0 Ricardo Wurmus
2018-03-01 18:41 ` [bug#30666] [PATCH 12/17] gnu: Add java-biojava-phylo-4.0 Ricardo Wurmus
2018-03-01 18:41 ` [bug#30666] [PATCH 13/17] gnu: Add java-biojava-alignment-4.0 Ricardo Wurmus
2018-03-01 18:41 ` Ricardo Wurmus [this message]
2018-03-01 18:41 ` [bug#30666] [PATCH 15/17] gnu: Add java-htsjdk-2.10.1 Ricardo Wurmus
2018-03-01 18:41 ` [bug#30666] [PATCH 16/17] gnu: Add java-picard-2.10.3 Ricardo Wurmus
2018-03-01 18:41 ` [bug#30666] [PATCH 17/17] gnu: Add dropseq-tools Ricardo Wurmus
[not found] ` <handler.30666.B.151992663330127.ack@debbugs.gnu.org>
2018-03-03 20:29 ` bug#30666: [PATCH 00/17] " Ricardo Wurmus
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