diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 114 |
1 files changed, 114 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 636e912ce5..833376ac21 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3086,6 +3086,120 @@ commonly used for high-throughput sequencing data such as SAM, BAM, CRAM and VCF.") (license license:expat))) +;; This is the last version of Picard to provide net.sf.samtools +(define-public java-picard-1.113 + (package (inherit java-picard) + (name "java-picard") + (version "1.113") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/broadinstitute/picard.git") + (commit version))) + (file-name (string-append "java-picard-" version "-checkout")) + (sha256 + (base32 + "0lkpvin2fz3hhly4l02kk56fqy8lmlgyzr9kmvljk6ry6l1hw973")) + (modules '((guix build utils))) + (snippet + '(begin + ;; Delete pre-built binaries. + (delete-file-recursively "lib") + (mkdir-p "lib") + #t)))) + (build-system ant-build-system) + (arguments + `(#:build-target "picard-jar" + #:test-target "test" + ;; FIXME: the class path at test time is wrong. + ;; [testng] Error: A JNI error has occurred, please check your installation and try again + ;; [testng] Exception in thread "main" java.lang.NoClassDefFoundError: com/beust/jcommander/ParameterException + #:tests? #f + #:jdk ,icedtea-8 + ;; This is only used for tests. + #:make-flags + (list "-Dsamjdk.intel_deflater_so_path=lib/jni/libIntelDeflater.so") + #:phases + (modify-phases %standard-phases + ;; Do not use bundled ant bzip2. + (add-after 'unpack 'use-ant-bzip + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "build.xml" + (("\\$\\{lib\\}/apache-ant-1.8.2-bzip2.jar") + (string-append (assoc-ref inputs "ant") + "/lib/ant.jar"))) + #t)) + (add-after 'unpack 'make-test-target-independent + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "build.xml" + (("name=\"test\" depends=\"compile, ") + "name=\"test\" depends=\"compile-tests, ") + (("name=\"compile\" depends=\"compile-src, compile-tests\"") + "name=\"compile\" depends=\"compile-src\"")) + #t)) + (add-after 'unpack 'fix-deflater-path + (lambda* (#:key outputs #:allow-other-keys) + (substitute* "src/java/net/sf/samtools/Defaults.java" + (("getStringProperty\\(\"intel_deflater_so_path\", null\\)") + (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. + (add-after 'build 'build-jni + (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++")))))) + ;; 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))))) + (add-before 'build 'set-JAVA6_HOME + (lambda _ + (setenv "JAVA6_HOME" (getenv "JAVA_HOME")) + #t)) + (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)))))) + (inputs + `(("java-snappy-1" ,java-snappy-1) + ("java-commons-jexl-2" ,java-commons-jexl-2) + ("java-cofoja" ,java-cofoja) + ("ant" ,ant) ; for bzip2 support at runtime + ("zlib" ,zlib))) + (native-inputs + `(("ant-apache-bcel" ,ant-apache-bcel) + ("ant-junit" ,ant-junit) + ("java-testng" ,java-testng) + ("java-commons-bcel" ,java-commons-bcel) + ("java-jcommander" ,java-jcommander) + ("jdk" ,icedtea-8 "jdk") + ("jdk-src" ,(car (assoc-ref (package-native-inputs icedtea-8) "jdk-drop"))))))) + (define-public htslib (package (name "htslib") |