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gnu: java-picard-1.113: Drop trailing #T from build phases.

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* gnu/packages/bioinformatics.scm (java-picard-1.113)[arguments]: Remove
trailing #T from build phases.
This commit is contained in:
Ricardo Wurmus 2023-05-19 13:10:37 +02:00
parent 61d7d9048f
commit 1baf94dbbe
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GPG key ID: 197A5888235FACAC
1 changed files with 7 additions and 14 deletions
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gnu/packages/bioinformatics.scm
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@ -5640,8 +5640,7 @@ VCF.")
'(begin '(begin
;; Delete pre-built binaries. ;; Delete pre-built binaries.
(delete-file-recursively "lib") (delete-file-recursively "lib")
(mkdir-p "lib") (mkdir-p "lib")))))
#t))))
(build-system ant-build-system) (build-system ant-build-system)
(arguments (arguments
`(#:build-target "picard-jar" `(#:build-target "picard-jar"
@ -5671,8 +5670,7 @@ VCF.")
(("name=\"test\" depends=\"compile, ") (("name=\"test\" depends=\"compile, ")
"name=\"test\" depends=\"compile-tests, ") "name=\"test\" depends=\"compile-tests, ")
(("name=\"compile\" depends=\"compile-src, compile-tests\"") (("name=\"compile\" depends=\"compile-src, compile-tests\"")
"name=\"compile\" depends=\"compile-src\"")) "name=\"compile\" depends=\"compile-src\""))))
#t))
(add-after 'unpack 'fix-deflater-path (add-after 'unpack 'fix-deflater-path
(lambda* (#:key outputs #:allow-other-keys) (lambda* (#:key outputs #:allow-other-keys)
(substitute* "src/java/net/sf/samtools/Defaults.java" (substitute* "src/java/net/sf/samtools/Defaults.java"
@ -5680,8 +5678,7 @@ VCF.")
(string-append "getStringProperty(\"intel_deflater_so_path\", \"" (string-append "getStringProperty(\"intel_deflater_so_path\", \""
(assoc-ref outputs "out") (assoc-ref outputs "out")
"/lib/jni/libIntelDeflater.so" "/lib/jni/libIntelDeflater.so"
"\")"))) "\")")))))
#t))
;; Build the deflater library, because we've previously deleted the ;; Build the deflater library, because we've previously deleted the
;; pre-built one. This can only be built with access to the JDK ;; pre-built one. This can only be built with access to the JDK
;; sources. ;; sources.
@ -5704,25 +5701,21 @@ VCF.")
"-c" "-O3" "-fPIC" "IntelDeflater.c") "-c" "-O3" "-fPIC" "IntelDeflater.c")
(invoke "gcc" "-shared" (invoke "gcc" "-shared"
"-o" "../../../lib/jni/libIntelDeflater.so" "-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. ;; We can only build everything else after building the JNI library.
(add-after 'build-jni 'build-rest (add-after 'build-jni 'build-rest
(lambda* (#:key make-flags #:allow-other-keys) (lambda* (#:key make-flags #:allow-other-keys)
(apply invoke `("ant" "all" ,@make-flags)) (apply invoke `("ant" "all" ,@make-flags))))
#t))
(add-before 'build 'set-JAVA6_HOME (add-before 'build 'set-JAVA6_HOME
(lambda _ (lambda _
(setenv "JAVA6_HOME" (getenv "JAVA_HOME")) (setenv "JAVA6_HOME" (getenv "JAVA_HOME"))))
#t))
(replace 'install (install-jars "dist")) (replace 'install (install-jars "dist"))
(add-after 'install 'install-jni-lib (add-after 'install 'install-jni-lib
(lambda* (#:key outputs #:allow-other-keys) (lambda* (#:key outputs #:allow-other-keys)
(let ((jni (string-append (assoc-ref outputs "out") (let ((jni (string-append (assoc-ref outputs "out")
"/lib/jni"))) "/lib/jni")))
(mkdir-p jni) (mkdir-p jni)
(install-file "lib/jni/libIntelDeflater.so" jni) (install-file "lib/jni/libIntelDeflater.so" jni)))))))
#t))))))
(inputs (inputs
`(("java-snappy-1" ,java-snappy-1) `(("java-snappy-1" ,java-snappy-1)
("java-commons-jexl-2" ,java-commons-jexl-2) ("java-commons-jexl-2" ,java-commons-jexl-2)