diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 24 |
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 |