diff options
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 28 |
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 |