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| author | Ludovic Courtès <ludo@gnu.org> | 2021-07-16 17:10:44 +0200 |
|---|---|---|
| committer | Ludovic Courtès <ludo@gnu.org> | 2021-07-24 16:23:23 +0200 |
| commit | 828cfdc47e567d75b4629a7af7afed3a20adcf5a (patch) | |
| tree | e47e198a53f3aecce175c21b3cc52b748f9abac1 /gnu/packages/bioinformatics.scm | |
| parent | 1ab95c2341ad0d0974f77657fe0426dcc64adffe (diff) | |
| download | guix-patches-828cfdc47e567d75b4629a7af7afed3a20adcf5a.tar guix-patches-828cfdc47e567d75b4629a7af7afed3a20adcf5a.tar.gz | |
gnu: Use 'search-input-file' when looking for .jar files.
* 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.
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 20 |
1 files changed, 8 insertions, 12 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 75668418f0..1719cf86ae 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -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) |