diff options
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 71 |
1 files changed, 34 insertions, 37 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1e7ce7eb60..265697d625 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5262,44 +5262,41 @@ VCF.") "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/") |