From 2651a5e6952785347f35f337b2cb65568d73d080 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 14 Apr 2015 14:24:01 +0200
Subject: [PATCH] gnu: Add NGS Java bindings.
* gnu/packages/bioinformatics.scm (ngs-java): New variable.
---
gnu/packages/bioinformatics.scm | 36 +++++++++++++++++++++++++++++++++
1 file changed, 36 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b5c557bb95f..4c4eedba2bd 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1087,6 +1087,42 @@ (define-public ngs-sdk
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")
--
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