gnu: Add NGS Java bindings.

* gnu/packages/bioinformatics.scm (ngs-java): New variable.
This commit is contained in:
Ricardo Wurmus 2015-04-14 14:24:01 +02:00
parent 282c5087b4
commit 2651a5e695
1 changed files with 36 additions and 0 deletions

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@ -1087,6 +1087,42 @@ any particular back-end implementation, and supports use of multiple back-ends
simultaneously.")
(license license:public-domain)))
(define-public ngs-java
(package (inherit ngs-sdk)
(name "ngs-java")
(arguments
`(,@(substitute-keyword-arguments
`(#:modules ((guix build gnu-build-system)
(guix build utils)
(srfi srfi-1)
(srfi srfi-26))
,@(package-arguments ngs-sdk))
((#:phases phases)
`(alist-cons-after
'enter-dir 'fix-java-symlink-installation
(lambda _
;; Only replace the version suffix, not the version number in
;; the directory name. Reported here:
;; https://github.com/ncbi/ngs/pull/4
(substitute* "Makefile.java"
(((string-append "\\$\\(subst "
"(\\$\\(VERSION[^\\)]*\\)),"
"(\\$\\([^\\)]+\\)),"
"(\\$\\([^\\)]+\\)|\\$\\@)"
"\\)")
_ pattern replacement target)
(string-append "$(patsubst "
"%" pattern ","
"%" replacement ","
target ")"))))
(alist-replace
'enter-dir (lambda _ (chdir "ngs-java") #t)
,phases))))))
(inputs
`(("jdk" ,icedtea6 "jdk")
("ngs-sdk" ,ngs-sdk)))
(synopsis "Java bindings for NGS SDK")))
(define-public seqan
(package
(name "seqan")