gnu: Add htsjdk.

* gnu/packages/bioinformatics.scm (htsjdk): New variable.
This commit is contained in:
Ricardo Wurmus 2015-03-05 10:24:12 +01:00
parent a79112079e
commit 15a3c3d4f1

View file

@ -27,6 +27,7 @@ (define-module (gnu packages bioinformatics)
#:use-module (gnu packages)
#:use-module (gnu packages base)
#:use-module (gnu packages compression)
#:use-module (gnu packages java)
#:use-module (gnu packages ncurses)
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
@ -446,6 +447,51 @@ (define-public htseq
from high-throughput sequencing assays.")
(license license:gpl3+)))
(define-public htsjdk
(package
(name "htsjdk")
(version "1.129")
(source (origin
(method url-fetch)
(uri (string-append
"https://github.com/samtools/htsjdk/archive/"
version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"0asdk9b8jx2ij7yd6apg9qx03li8q7z3ml0qy2r2qczkra79y6fw"))
(modules '((guix build utils)))
;; remove build dependency on git
(snippet '(substitute* "build.xml"
(("failifexecutionfails=\"true\"")
"failifexecutionfails=\"false\"")))))
(build-system gnu-build-system)
(arguments
`(#:modules ((srfi srfi-1)
(guix build gnu-build-system)
(guix build utils))
#:phases (alist-replace
'build
(lambda _
(setenv "JAVA_HOME" (assoc-ref %build-inputs "jdk"))
(zero? (system* "ant" "all"
(string-append "-Ddist="
(assoc-ref %outputs "out")
"/share/java/htsjdk/"))))
(fold alist-delete %standard-phases
'(configure install check)))))
(native-inputs
`(("ant" ,ant)
("jdk" ,icedtea6 "jdk")))
(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)))
(define-public macs
(package
(name "macs")