diff options
Diffstat (limited to 'gn/packages/bioinformatics.scm')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 57 |
1 files changed, 57 insertions, 0 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index a4d14b0..1f6052e 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -6,6 +6,7 @@ #:use-module (guix utils) #:use-module (guix download) #:use-module (guix git-download) + #:use-module (guix build-system ant) #:use-module (guix build-system gnu) #:use-module (guix build-system cmake) #:use-module (guix build-system perl) @@ -1287,3 +1288,59 @@ single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.") (license license:gpl3+))) + +(define-public varscan + (package + (name "varscan") + (version "2.4.1") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/dkoboldt/varscan/releases/download/v" + version "/VarScan.v" version ".source.jar")) + (sha256 + (base32 "0y45ympkza7qwcbcisg006286pwjbr5978n03hx5nvl09f0mapk8")))) + (build-system ant-build-system) + (arguments + `(#: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)))))) + (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"))))))) + (replace 'install + (lambda _ + (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/") + (synopsis "Variant detection in massively parallel sequencing data") + (description "") + ;; Free for non-commercial use by academic, government, and + ;; non-profit/not-for-profit institutions + (license license:non-copyleft))) |