@@ 27,6 27,7 @@
#: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 @@ particular, reads spanning multiple exons.")
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")