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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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21
gnu/packages/bioinformatics.scm
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@ -5640,8 +5640,7 @@ (define-public java-picard-1.113
'(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 @@ (define-public java-picard-1.113
(("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 @@ (define-public java-picard-1.113
(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 @@ (define-public java-picard-1.113
"-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)