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authorEfraim Flashner2019-08-05 07:41:00 -0500
committerEfraim Flashner2019-08-05 07:41:00 -0500
commitb0926f0df4f76b24dbb99da3f10a87e606fac993 (patch)
treeb3b24e160047becde398a0cfeb9eee8f10d2ad6d
parenta2332e54719b069378fc2c54beae03e81aad97d4 (diff)
downloadguix-bioinformatics-b0926f0df4f76b24dbb99da3f10a87e606fac993.tar.gz
gn: varscan: Fix build.
* gn/packages/bioinformatics.scm (varscan)[arguments]: Disable tests. Update all custom phases. [home-page]: Use https. [description]: Add it.
-rw-r--r--gn/packages/bioinformatics.scm55
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)))