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gnu: fastqc: Update to 0.11.9.

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* gnu/packages/bioinformatics.scm (fastqc): Update to 0.11.9.
[source]: Fetch via git; delete bundled jar files.
[arguments]: Also patch .classpath file in 'fix-dependencies; fix patching of
reference to java in fastqc wrapper; override CLASSPATH.
This commit is contained in:
Ricardo Wurmus 2023-02-14 13:32:58 +01:00
parent 1b4f6286df
commit b6a4fbb488
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GPG key ID: 197A5888235FACAC
1 changed files with 29 additions and 12 deletions
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41
gnu/packages/bioinformatics.scm
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@ -5250,16 +5250,22 @@ VCF.")
(define-public fastqc (define-public fastqc
(package (package
(name "fastqc") (name "fastqc")
(version "0.11.5") (version "0.11.9")
(source (source
(origin (origin
(method url-fetch) (method git-fetch)
(uri (string-append "http://www.bioinformatics.babraham.ac.uk/" (uri (git-reference
"projects/fastqc/fastqc_v" (url "https://github.com/s-andrews/FastQC")
version "_source.zip")) (commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256 (sha256
(base32 (base32
"18rrlkhcrxvvvlapch4dpj6xc6mpayzys8qfppybi8jrpgx5cc5f")))) "00y9drm0bkpxw8xfl8ysss18jmnhj8blgqgr6fpa58rkpfcbg8qk"))
(snippet
'(for-each delete-file
'("cisd-jhdf5.jar"
"sam-1.103.jar"
"jbzip2-0.9.jar")))))
(build-system ant-build-system) (build-system ant-build-system)
(arguments (arguments
(list (list
@ -5269,7 +5275,7 @@ VCF.")
#~(modify-phases %standard-phases #~(modify-phases %standard-phases
(add-after 'unpack 'fix-dependencies (add-after 'unpack 'fix-dependencies
(lambda* (#:key inputs #:allow-other-keys) (lambda* (#:key inputs #:allow-other-keys)
(substitute* "build.xml" (substitute* '("build.xml" ".classpath")
(("jbzip2-0.9.jar") (("jbzip2-0.9.jar")
(search-input-file inputs "/share/java/jbzip2.jar")) (search-input-file inputs "/share/java/jbzip2.jar"))
(("sam-1.103.jar") (("sam-1.103.jar")
@ -5278,17 +5284,28 @@ VCF.")
(search-input-file inputs "/share/java/sis-jhdf5.jar"))))) (search-input-file inputs "/share/java/sis-jhdf5.jar")))))
;; There is no installation target ;; There is no installation target
(replace 'install (replace 'install
(lambda* (#:key inputs outputs #:allow-other-keys) (lambda* (#:key inputs #:allow-other-keys)
(let* ((bin (string-append #$output "/bin")) (let* ((bin (string-append #$output "/bin"))
(share (string-append #$output "/share/fastqc/")) (share (string-append #$output "/share/fastqc/"))
(exe (string-append share "/fastqc"))) (exe (string-append share "/fastqc")))
(for-each mkdir-p (list bin share)) (for-each mkdir-p (list bin share))
(copy-recursively "bin" share) (copy-recursively "bin" share)
(substitute* exe (substitute* exe
(("my \\$java_bin = 'java';") (("my \\$java_bin = \"java\";")
(string-append "my $java_bin = '" (string-append "my $java_bin = \""
(search-input-file inputs "/bin/java") ;; Use java from the JRE, not the JDK
"';"))) #$(this-package-input "icedtea") "/bin/java"
"\";"))
(("\\$RealBin\\$delimiter\\$RealBin.*")
(string-append
(string-join
(list
share
(search-input-file inputs "/share/java/sam-1.112.jar")
(search-input-file inputs "/share/java/jbzip2.jar")
(search-input-file inputs "/share/java/sis-jhdf5.jar"))
"$delimiter")
"\";\n")))
(chmod exe #o555) (chmod exe #o555)
(symlink exe (string-append bin "/fastqc")))))))) (symlink exe (string-append bin "/fastqc"))))))))
(inputs (inputs