diff options
| -rw-r--r-- | gn/packages/bioinformatics.scm | 55 |
1 files changed, 26 insertions, 29 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index e5914c2..b7db927 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -881,45 +881,42 @@ reads.") (base32 "0y45ympkza7qwcbcisg006286pwjbr5978n03hx5nvl09f0mapk8")))) (build-system ant-build-system) (arguments - `(#:phases + `(#:tests? #f ; build.xml does not exist + #:phases (modify-phases %standard-phases (replace 'unpack (lambda _ (mkdir "source") (chdir "source") - (and - ;; Unpack the Java archive containing the source files. - (zero? (system* "jar" "xf" (assoc-ref %build-inputs "source"))) - ;; Remove existing compiled output. - (with-directory-excursion "net/sf/varscan/" - (for-each (lambda (file) - (unless (string= (string-take-right file 5) ".java") - (zero? (system* "rm" file)))) - (find-files "." #:directories? #f)))))) + ;; Unpack the Java archive containing the source files. + (invoke "jar" "xf" (assoc-ref %build-inputs "source")) + ;; Remove existing compiled output. + (with-directory-excursion "net/sf/varscan/" + (for-each (lambda (file) + (delete-file file)) + (find-files "." "^.java$" #:directories? #f))) + #t)) (replace 'build (lambda _ - (let ((classes '())) - (and - ;; Compile the source files. - (with-directory-excursion "net/sf/varscan/" - (for-each (lambda (file) - (when (string= (string-take-right file 5) ".java") - (zero? (system* "javac" file)) - (cons )) - (find-files "." #:directories? #f))) - ;; Construct the new Java archive. - (zero? (system* "jar" "cfm" "varscan-2.4.1.jar" - "META-INF/MANIFEST.MF" - "net/sf/varscan/*.java"))))))) + ;; Compile the source files. + (with-directory-excursion "net/sf/varscan/" + (for-each (lambda (file) + (invoke "javac" file)) + (find-files "." ".java$" #:directories? #f))) + ;; Construct the new Java archive. + (apply invoke "jar" "cfm" + (string-append "varscan-" ,version ".jar") + "META-INF/MANIFEST.MF" + (find-files "net/sf/varscan" ".java$")))) (replace 'install - (lambda _ - (let ((out (string-append (assoc-ref %outputs "out") + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (string-append (assoc-ref outputs "out") "/share/java/varscan/"))) - (mkdir-p out) - (install-file "varscan-2.4.1.jar" out))))))) - (home-page "http://dkoboldt.github.io/varscan/") + (install-file (string-append "varscan-" ,version ".jar") out)) + #t))))) + (home-page "https://dkoboldt.github.io/varscan/") (synopsis "Variant detection in massively parallel sequencing data") - (description "") + (description "Variant detection in massively parallel sequencing data.") ;; Free for non-commercial use by academic, government, and ;; non-profit/not-for-profit institutions (license license:non-copyleft))) |