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gnu: fastqc: Use gexp.

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* gnu/packages/bioinformatics.scm (fastqc)[arguments]: Use gexp; drop
trailing #T from build phase.
[inputs]: Drop package labels.
This commit is contained in:
Ricardo Wurmus 2023-02-13 22:34:37 +01:00
parent 47f0e022dc
commit 7260cc75da
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GPG key ID: 197A5888235FACAC
1 changed files with 34 additions and 37 deletions
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gnu/packages/bioinformatics.scm
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@ -5262,44 +5262,41 @@ (define-public fastqc
"18rrlkhcrxvvvlapch4dpj6xc6mpayzys8qfppybi8jrpgx5cc5f"))))
(build-system ant-build-system)
(arguments
`(#:tests? #f ; there are no tests
#:build-target "build"
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'fix-dependencies
(lambda* (#:key inputs #:allow-other-keys)
(substitute* "build.xml"
(("jbzip2-0.9.jar")
(search-input-file inputs "/share/java/jbzip2.jar"))
(("sam-1.103.jar")
(search-input-file inputs
"/share/java/sam-1.112.jar"))
(("cisd-jhdf5.jar")
(search-input-file inputs
"/share/java/sis-jhdf5.jar")))))
;; There is no installation target
(replace 'install
(lambda* (#:key inputs outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(bin (string-append out "/bin"))
(share (string-append out "/share/fastqc/"))
(exe (string-append share "/fastqc")))
(for-each mkdir-p (list bin share))
(copy-recursively "bin" share)
(substitute* exe
(("my \\$java_bin = 'java';")
(string-append "my $java_bin = '"
(assoc-ref inputs "java")
"/bin/java';")))
(chmod exe #o555)
(symlink exe (string-append bin "/fastqc"))
#t))))))
(list
#:tests? #f ;there are no tests
#:build-target "build"
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'fix-dependencies
(lambda* (#:key inputs #:allow-other-keys)
(substitute* "build.xml"
(("jbzip2-0.9.jar")
(search-input-file inputs "/share/java/jbzip2.jar"))
(("sam-1.103.jar")
(search-input-file inputs "/share/java/sam-1.112.jar"))
(("cisd-jhdf5.jar")
(search-input-file inputs "/share/java/sis-jhdf5.jar")))))
;; There is no installation target
(replace 'install
(lambda* (#:key inputs outputs #:allow-other-keys)
(let* ((bin (string-append #$output "/bin"))
(share (string-append #$output "/share/fastqc/"))
(exe (string-append share "/fastqc")))
(for-each mkdir-p (list bin share))
(copy-recursively "bin" share)
(substitute* exe
(("my \\$java_bin = 'java';")
(string-append "my $java_bin = '"
(search-input-file inputs "/bin/java")
"';")))
(chmod exe #o555)
(symlink exe (string-append bin "/fastqc"))))))))
(inputs
`(("java" ,icedtea)
("perl" ,perl) ; needed for the wrapper script
("java-cisd-jhdf5" ,java-cisd-jhdf5)
("java-picard-1.113" ,java-picard-1.113)
("java-jbzip2" ,java-jbzip2)))
(list icedtea
java-cisd-jhdf5
java-picard-1.113
java-jbzip2
perl)) ;needed for the wrapper script
(native-inputs
(list unzip))
(home-page "https://www.bioinformatics.babraham.ac.uk/projects/fastqc/")