diff options
| author | Ricardo Wurmus <rekado@elephly.net> | 2023-02-14 13:32:58 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2023-02-16 16:56:10 +0100 |
| commit | b6a4fbb488f1f539ae45ed7924c9af8905fa0d8b (patch) | |
| tree | 633e026cdef9e7f7577cdb4a07e0fbc535ec7335 /gnu | |
| parent | 1b4f6286df13505cd17b3060fe4da7f03f39ba59 (diff) | |
gnu: fastqc: Update to 0.11.9.
* 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.
Diffstat (limited to 'gnu')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 41 |
1 files changed, 29 insertions, 12 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c6eab671cb..5b9d754060 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5250,16 +5250,22 @@ VCF.") (define-public fastqc (package (name "fastqc") - (version "0.11.5") + (version "0.11.9") (source (origin - (method url-fetch) - (uri (string-append "http://www.bioinformatics.babraham.ac.uk/" - "projects/fastqc/fastqc_v" - version "_source.zip")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/s-andrews/FastQC") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "18rrlkhcrxvvvlapch4dpj6xc6mpayzys8qfppybi8jrpgx5cc5f")))) + "00y9drm0bkpxw8xfl8ysss18jmnhj8blgqgr6fpa58rkpfcbg8qk")) + (snippet + '(for-each delete-file + '("cisd-jhdf5.jar" + "sam-1.103.jar" + "jbzip2-0.9.jar"))))) (build-system ant-build-system) (arguments (list @@ -5269,7 +5275,7 @@ VCF.") #~(modify-phases %standard-phases (add-after 'unpack 'fix-dependencies (lambda* (#:key inputs #:allow-other-keys) - (substitute* "build.xml" + (substitute* '("build.xml" ".classpath") (("jbzip2-0.9.jar") (search-input-file inputs "/share/java/jbzip2.jar")) (("sam-1.103.jar") @@ -5278,17 +5284,28 @@ VCF.") (search-input-file inputs "/share/java/sis-jhdf5.jar"))))) ;; There is no installation target (replace 'install - (lambda* (#:key inputs outputs #:allow-other-keys) + (lambda* (#:key inputs #: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 $java_bin = '" - (search-input-file inputs "/bin/java") - "';"))) + (("my \\$java_bin = \"java\";") + (string-append "my $java_bin = \"" + ;; Use java from the JRE, not the JDK + #$(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) (symlink exe (string-append bin "/fastqc")))))))) (inputs |