diff options
Diffstat (limited to 'gnu')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 21 |
1 files changed, 7 insertions, 14 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b2d0f90761..1e7404549b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5640,8 +5640,7 @@ VCF.") '(begin ;; Delete pre-built binaries. (delete-file-recursively "lib") - (mkdir-p "lib") - #t)))) + (mkdir-p "lib"))))) (build-system ant-build-system) (arguments `(#:build-target "picard-jar" @@ -5671,8 +5670,7 @@ VCF.") (("name=\"test\" depends=\"compile, ") "name=\"test\" depends=\"compile-tests, ") (("name=\"compile\" depends=\"compile-src, compile-tests\"") - "name=\"compile\" depends=\"compile-src\"")) - #t)) + "name=\"compile\" depends=\"compile-src\"")))) (add-after 'unpack 'fix-deflater-path (lambda* (#:key outputs #:allow-other-keys) (substitute* "src/java/net/sf/samtools/Defaults.java" @@ -5680,8 +5678,7 @@ VCF.") (string-append "getStringProperty(\"intel_deflater_so_path\", \"" (assoc-ref outputs "out") "/lib/jni/libIntelDeflater.so" - "\")"))) - #t)) + "\")"))))) ;; Build the deflater library, because we've previously deleted the ;; pre-built one. This can only be built with access to the JDK ;; sources. @@ -5704,25 +5701,21 @@ VCF.") "-c" "-O3" "-fPIC" "IntelDeflater.c") (invoke "gcc" "-shared" "-o" "../../../lib/jni/libIntelDeflater.so" - "IntelDeflater.o" "-lz" "-lstdc++")) - #t)) + "IntelDeflater.o" "-lz" "-lstdc++")))) ;; We can only build everything else after building the JNI library. (add-after 'build-jni 'build-rest (lambda* (#:key make-flags #:allow-other-keys) - (apply invoke `("ant" "all" ,@make-flags)) - #t)) + (apply invoke `("ant" "all" ,@make-flags)))) (add-before 'build 'set-JAVA6_HOME (lambda _ - (setenv "JAVA6_HOME" (getenv "JAVA_HOME")) - #t)) + (setenv "JAVA6_HOME" (getenv "JAVA_HOME")))) (replace 'install (install-jars "dist")) (add-after 'install 'install-jni-lib (lambda* (#:key outputs #:allow-other-keys) (let ((jni (string-append (assoc-ref outputs "out") "/lib/jni"))) (mkdir-p jni) - (install-file "lib/jni/libIntelDeflater.so" jni) - #t)))))) + (install-file "lib/jni/libIntelDeflater.so" jni))))))) (inputs `(("java-snappy-1" ,java-snappy-1) ("java-commons-jexl-2" ,java-commons-jexl-2) |