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authorRicardo Wurmus <ricardo.wurmus@mdc-berlin.de>2016-03-14 13:02:48 +0100
committerRicardo Wurmus <ricardo.wurmus@mdc-berlin.de>2016-03-14 14:30:03 +0100
commit10b4a969beb6e5ae22faa314ba9ef5a2ea7639b1 (patch)
tree93c55a9b7383b0d72f6767fa674d16925855afe2 /gnu
parent5f7a1a4def8494940a4a2bc3728fb9cd927a14f8 (diff)
gnu: htsjdk: Use ant-build-system.
* gnu/packages/bioinformatics.scm (htsjdk)[build-system]: Use ant-build-system. [arguments]: Adapt for ant-build-system.
Diffstat (limited to 'gnu')
-rw-r--r--gnu/packages/bioinformatics.scm28
1 files changed, 11 insertions, 17 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4925290910..4dd2ee6f92 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -26,6 +26,7 @@
#:use-module (guix utils)
#:use-module (guix download)
#:use-module (guix git-download)
+ #:use-module (guix build-system ant)
#:use-module (guix build-system gnu)
#:use-module (guix build-system cmake)
#:use-module (guix build-system perl)
@@ -2002,24 +2003,17 @@ from high-throughput sequencing assays.")
(snippet '(substitute* "build.xml"
(("failifexecutionfails=\"true\"")
"failifexecutionfails=\"false\"")))))
- (build-system gnu-build-system)
+ (build-system ant-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" ,icedtea "jdk")))
+ `(#:tests? #f ; test require Internet access
+ #:make-flags
+ (list (string-append "-Ddist=" (assoc-ref %outputs "out")
+ "/share/java/htsjdk/"))
+ #:build-target "all"
+ #:phases
+ (modify-phases %standard-phases
+ ;; The build phase also installs the jars
+ (delete 'install))))
(home-page "http://samtools.github.io/htsjdk/")
(synopsis "Java API for high-throughput sequencing data (HTS) formats")
(description