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| author | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2015-04-14 14:24:01 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2015-04-20 15:29:16 +0200 |
| commit | 2651a5e6952785347f35f337b2cb65568d73d080 (patch) | |
| tree | 6508732fd03cbc1bf94967175ea23a40bbc46a72 /gnu/packages | |
| parent | 282c5087b4be022b832cf73f43942bca924c3006 (diff) | |
| download | gnu-guix-2651a5e6952785347f35f337b2cb65568d73d080.tar gnu-guix-2651a5e6952785347f35f337b2cb65568d73d080.tar.gz | |
gnu: Add NGS Java bindings.
* gnu/packages/bioinformatics.scm (ngs-java): New variable.
Diffstat (limited to 'gnu/packages')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 36 |
1 files changed, 36 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b5c557bb95..4c4eedba2b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -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") |