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authorRicardo Wurmus <rekado@elephly.net>2017-11-18 23:58:59 +0100
committerRicardo Wurmus <rekado@elephly.net>2017-11-27 12:12:40 +0100
commitbd94b6f850b2be6953a2d8688b2be78cac8d341a (patch)
treec8823171fea1e1ca6b3292372bdfa647db7f0e99 /gnu
parent9e325e8c05f39a020b620066172625d67c04a9e3 (diff)
downloadguix-bd94b6f850b2be6953a2d8688b2be78cac8d341a.tar
guix-bd94b6f850b2be6953a2d8688b2be78cac8d341a.tar.gz
gnu: java-htsjdk: Update to 2.3.0.
* gnu/packages/bioinformatics.scm (java-htsjdk): Update to 2.3.0. [arguments]: Build with JDK 8. [inputs]: Add java-ngs, java-snappy, java-commons-compress, java-commons-logging-minimal, java-commons-jexl-2, and java-xz. [native-inputs]: Add java-testng.
Diffstat (limited to 'gnu')
-rw-r--r--gnu/packages/bioinformatics.scm24
1 files changed, 18 insertions, 6 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 2a2d7f8ff7..5164da0ef7 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2961,7 +2961,7 @@ from high-throughput sequencing assays.")
(define-public java-htsjdk
(package
(name "java-htsjdk")
- (version "1.129")
+ (version "2.3.0") ; last version without build dependency on gradle
(source (origin
(method url-fetch)
(uri (string-append
@@ -2970,15 +2970,18 @@ from high-throughput sequencing assays.")
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "0asdk9b8jx2ij7yd6apg9qx03li8q7z3ml0qy2r2qczkra79y6fw"))
+ "1ibhzzxsfc38nqyk9r8zqj6blfc1kh26iirypd4q6n90hs2m6nyq"))
(modules '((guix build utils)))
- ;; remove build dependency on git
- (snippet '(substitute* "build.xml"
- (("failifexecutionfails=\"true\"")
- "failifexecutionfails=\"false\"")))))
+ (snippet
+ ;; Delete pre-built binaries
+ '(begin
+ (delete-file-recursively "lib")
+ (mkdir-p "lib")
+ #t))))
(build-system ant-build-system)
(arguments
`(#:tests? #f ; test require Internet access
+ #:jdk ,icedtea-8
#:make-flags
(list (string-append "-Ddist=" (assoc-ref %outputs "out")
"/share/java/htsjdk/"))
@@ -2987,6 +2990,15 @@ from high-throughput sequencing assays.")
(modify-phases %standard-phases
;; The build phase also installs the jars
(delete 'install))))
+ (inputs
+ `(("java-ngs" ,java-ngs)
+ ("java-snappy-1" ,java-snappy-1)
+ ("java-commons-compress" ,java-commons-compress)
+ ("java-commons-logging-minimal" ,java-commons-logging-minimal)
+ ("java-commons-jexl-2" ,java-commons-jexl-2)
+ ("java-xz" ,java-xz)))
+ (native-inputs
+ `(("java-testng" ,java-testng)))
(home-page "http://samtools.github.io/htsjdk/")
(synopsis "Java API for high-throughput sequencing data (HTS) formats")
(description