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gnu: java-picard-1.113: Use INVOKE. 

* gnu/packages/bioinformatics.scm (java-picard-1.113)[arguments]: Use INVOKE
and return #T unconditionally.
This commit is contained in:
Ricardo Wurmus 2018-11-08 09:02:34 +01:00
parent e438c96558
commit c527d36f02
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1 changed files with 19 additions and 17 deletions
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@ -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"
(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"))
"net.sf.samtools.util.zip.IntelDeflater")
(with-directory-excursion "src/c/inteldeflater"
(zero? (system* "gcc" "-I../../../lib" "-I."
(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"))
(zero? (system* "gcc" "-shared"
"-c" "-O3" "-fPIC" "IntelDeflater.c")
(invoke "gcc" "-shared"
"-o" "../../../lib/jni/libIntelDeflater.so"
"IntelDeflater.o" "-lz" "-lstdc++"))))))
"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"))