gnu: Add java-picard-1.113.
* gnu/packages/bioinformatics.scm (java-picard-1.113): New variable.
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@ -3086,6 +3086,120 @@ (define-public java-picard
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VCF.")
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(license license:expat)))
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;; This is the last version of Picard to provide net.sf.samtools
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(define-public java-picard-1.113
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(package (inherit java-picard)
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(name "java-picard")
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(version "1.113")
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(source (origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/broadinstitute/picard.git")
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(commit version)))
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(file-name (string-append "java-picard-" version "-checkout"))
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(sha256
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(base32
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"0lkpvin2fz3hhly4l02kk56fqy8lmlgyzr9kmvljk6ry6l1hw973"))
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(modules '((guix build utils)))
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(snippet
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'(begin
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;; Delete pre-built binaries.
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(delete-file-recursively "lib")
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(mkdir-p "lib")
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#t))))
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(build-system ant-build-system)
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(arguments
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`(#:build-target "picard-jar"
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#:test-target "test"
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;; FIXME: the class path at test time is wrong.
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;; [testng] Error: A JNI error has occurred, please check your installation and try again
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;; [testng] Exception in thread "main" java.lang.NoClassDefFoundError: com/beust/jcommander/ParameterException
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#:tests? #f
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#:jdk ,icedtea-8
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;; This is only used for tests.
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#:make-flags
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(list "-Dsamjdk.intel_deflater_so_path=lib/jni/libIntelDeflater.so")
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#:phases
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(modify-phases %standard-phases
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;; Do not use bundled ant bzip2.
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(add-after 'unpack 'use-ant-bzip
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(lambda* (#:key inputs #:allow-other-keys)
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(substitute* "build.xml"
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(("\\$\\{lib\\}/apache-ant-1.8.2-bzip2.jar")
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(string-append (assoc-ref inputs "ant")
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"/lib/ant.jar")))
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#t))
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(add-after 'unpack 'make-test-target-independent
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(lambda* (#:key inputs #:allow-other-keys)
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(substitute* "build.xml"
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(("name=\"test\" depends=\"compile, ")
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"name=\"test\" depends=\"compile-tests, ")
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(("name=\"compile\" depends=\"compile-src, compile-tests\"")
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"name=\"compile\" depends=\"compile-src\""))
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#t))
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(add-after 'unpack 'fix-deflater-path
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(lambda* (#:key outputs #:allow-other-keys)
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(substitute* "src/java/net/sf/samtools/Defaults.java"
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(("getStringProperty\\(\"intel_deflater_so_path\", null\\)")
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(string-append "getStringProperty(\"intel_deflater_so_path\", \""
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(assoc-ref outputs "out")
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"/lib/jni/libIntelDeflater.so"
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"\")")))
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#t))
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;; Build the deflater library, because we've previously deleted the
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;; pre-built one. This can only be built with access to the JDK
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;; sources.
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(add-after 'build 'build-jni
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(lambda* (#:key inputs #:allow-other-keys)
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(mkdir-p "lib/jni")
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(mkdir-p "jdk-src")
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(and (zero? (system* "tar" "--strip-components=1" "-C" "jdk-src"
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"-xf" (assoc-ref inputs "jdk-src")))
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(zero? (system* "javah" "-jni"
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"-classpath" "classes"
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"-d" "lib/"
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"net.sf.samtools.util.zip.IntelDeflater"))
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(with-directory-excursion "src/c/inteldeflater"
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(zero? (system* "gcc" "-I../../../lib" "-I."
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(string-append "-I" (assoc-ref inputs "jdk")
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"/include/linux")
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"-I../../../jdk-src/src/share/native/common/"
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"-I../../../jdk-src/src/solaris/native/common/"
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"-c" "-O3" "-fPIC" "IntelDeflater.c"))
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(zero? (system* "gcc" "-shared"
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"-o" "../../../lib/jni/libIntelDeflater.so"
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"IntelDeflater.o" "-lz" "-lstdc++"))))))
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;; We can only build everything else after building the JNI library.
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(add-after 'build-jni 'build-rest
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(lambda* (#:key make-flags #:allow-other-keys)
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(zero? (apply system* `("ant" "all" ,@make-flags)))))
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(add-before 'build 'set-JAVA6_HOME
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(lambda _
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(setenv "JAVA6_HOME" (getenv "JAVA_HOME"))
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#t))
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(replace 'install (install-jars "dist"))
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(add-after 'install 'install-jni-lib
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(lambda* (#:key outputs #:allow-other-keys)
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(let ((jni (string-append (assoc-ref outputs "out")
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"/lib/jni")))
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(mkdir-p jni)
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(install-file "lib/jni/libIntelDeflater.so" jni)
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#t))))))
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(inputs
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`(("java-snappy-1" ,java-snappy-1)
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("java-commons-jexl-2" ,java-commons-jexl-2)
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("java-cofoja" ,java-cofoja)
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("ant" ,ant) ; for bzip2 support at runtime
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("zlib" ,zlib)))
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(native-inputs
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`(("ant-apache-bcel" ,ant-apache-bcel)
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("ant-junit" ,ant-junit)
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("java-testng" ,java-testng)
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("java-commons-bcel" ,java-commons-bcel)
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("java-jcommander" ,java-jcommander)
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("jdk" ,icedtea-8 "jdk")
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("jdk-src" ,(car (assoc-ref (package-native-inputs icedtea-8) "jdk-drop")))))))
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(define-public htslib
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(package
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(name "htslib")
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