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| author | Ricardo Wurmus <rekado@elephly.net> | 2018-11-08 09:02:34 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2018-11-08 09:02:34 +0100 |
| commit | c527d36f0250b9815507e4ac28c3d7cfb6b87b20 (patch) | |
| tree | 797cb073cf99500a6ccca8abf0786a3f6e83e89e /gnu/packages/bioinformatics.scm | |
| parent | e438c9655808c0c3f1a56b7c5a17954670fd365d (diff) | |
| download | patches-c527d36f0250b9815507e4ac28c3d7cfb6b87b20.tar patches-c527d36f0250b9815507e4ac28c3d7cfb6b87b20.tar.gz | |
gnu: java-picard-1.113: Use INVOKE.
* gnu/packages/bioinformatics.scm (java-picard-1.113)[arguments]: Use INVOKE
and return #T unconditionally.
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 36 |
1 files changed, 19 insertions, 17 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e1ed7117f2..70597e2bcb 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3476,26 +3476,28 @@ VCF.") (lambda* (#:key inputs #:allow-other-keys) (mkdir-p "lib/jni") (mkdir-p "jdk-src") - (and (zero? (system* "tar" "--strip-components=1" "-C" "jdk-src" - "-xf" (assoc-ref inputs "jdk-src"))) - (zero? (system* "javah" "-jni" - "-classpath" "classes" - "-d" "lib/" - "net.sf.samtools.util.zip.IntelDeflater")) - (with-directory-excursion "src/c/inteldeflater" - (zero? (system* "gcc" "-I../../../lib" "-I." - (string-append "-I" (assoc-ref inputs "jdk") - "/include/linux") - "-I../../../jdk-src/src/share/native/common/" - "-I../../../jdk-src/src/solaris/native/common/" - "-c" "-O3" "-fPIC" "IntelDeflater.c")) - (zero? (system* "gcc" "-shared" - "-o" "../../../lib/jni/libIntelDeflater.so" - "IntelDeflater.o" "-lz" "-lstdc++")))))) + (invoke "tar" "--strip-components=1" "-C" "jdk-src" + "-xf" (assoc-ref inputs "jdk-src")) + (invoke "javah" "-jni" + "-classpath" "classes" + "-d" "lib/" + "net.sf.samtools.util.zip.IntelDeflater") + (with-directory-excursion "src/c/inteldeflater" + (invoke "gcc" "-I../../../lib" "-I." + (string-append "-I" (assoc-ref inputs "jdk") + "/include/linux") + "-I../../../jdk-src/src/share/native/common/" + "-I../../../jdk-src/src/solaris/native/common/" + "-c" "-O3" "-fPIC" "IntelDeflater.c") + (invoke "gcc" "-shared" + "-o" "../../../lib/jni/libIntelDeflater.so" + "IntelDeflater.o" "-lz" "-lstdc++")) + #t)) ;; We can only build everything else after building the JNI library. (add-after 'build-jni 'build-rest (lambda* (#:key make-flags #:allow-other-keys) - (zero? (apply system* `("ant" "all" ,@make-flags))))) + (apply invoke `("ant" "all" ,@make-flags)) + #t)) (add-before 'build 'set-JAVA6_HOME (lambda _ (setenv "JAVA6_HOME" (getenv "JAVA_HOME")) |