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gnu: Use 'search-input-file' when looking for .jar files.

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* gnu/packages/bioinformatics.scm (java-picard-1.113): Use
'search-input-file' when looking for *.jar.
(fastqc): Likewise.
* gnu/packages/groovy.scm (groovy): Likewise.
* gnu/packages/java.scm (ant-bootstrap): Likewise.
(ecj-bootstrap): Likewise.
(java-cisd-base): Likewise.
(java-cisd-args4j): Likewise.
(java-cisd-jhdf5): Likewise.
(java-native-access): Likewise.
(java-native-access-platform): Likewise.
* gnu/packages/maths.scm (hdf-java): Likewise.
This commit is contained in:
Ludovic Courtès 2021-07-16 17:10:44 +02:00
parent 1ab95c2341
commit 828cfdc47e
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4 changed files with 49 additions and 52 deletions
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20
gnu/packages/bioinformatics.scm
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@ -4379,9 +4379,7 @@ VCF.")
(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))
(search-input-file inputs "/lib/ant.jar")))))
(add-after 'unpack 'make-test-target-independent
(lambda* (#:key inputs #:allow-other-keys)
(substitute* "build.xml"
@ -4478,15 +4476,13 @@ VCF.")
(lambda* (#:key inputs #:allow-other-keys)
(substitute* "build.xml"
(("jbzip2-0.9.jar")
(string-append (assoc-ref inputs "java-jbzip2")
"/share/java/jbzip2.jar"))
(search-input-file inputs "/share/java/jbzip2.jar"))
(("sam-1.103.jar")
(string-append (assoc-ref inputs "java-picard-1.113")
"/share/java/sam-1.112.jar"))
(search-input-file inputs
"/share/java/sam-1.112.jar"))
(("cisd-jhdf5.jar")
(string-append (assoc-ref inputs "java-cisd-jhdf5")
"/share/java/sis-jhdf5.jar")))
#t))
(search-input-file inputs
"/share/java/sis-jhdf5.jar")))))
;; There is no installation target
(replace 'install
(lambda* (#:key inputs outputs #:allow-other-keys)
@ -9137,8 +9133,8 @@ browser.")
(substitute* "bin/linux/fseq"
(("java") (which "java"))
(("\\$REALDIR/../lib/commons-cli-1.1.jar")
(string-append (assoc-ref inputs "java-commons-cli")
"/share/java/commons-cli.jar"))
(search-input-file inputs
"/share/java/commons-cli.jar"))
(("REALDIR=.*")
(string-append "REALDIR=" bin "\n")))
(install-file "README.txt" doc)