(address . guix-patches@gnu.org)(name . Ricardo Wurmus)(address . ricardo.wurmus@mdc-berlin.de)
20170615152624.26092-1-ricardo.wurmus@mdc-berlin.de
* gnu/packages/bioinformatics.scm (f-seq): New variable.
---
gnu/packages/bioinformatics.scm | 50 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 50 insertions(+)
Toggle diff (60 lines)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index c1c0faf24..4c81f0741 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9655,3 +9655,53 @@ browser.")
(license (license:non-copyleft
"http://genome.ucsc.edu/license/"
"The contents of this package are free for all uses."))))
+
+(define-public f-seq
+ (let ((commit "6ccded34cff38cf432deed8503648b4a66953f9b")
+ (revision "1"))
+ (package
+ (name "f-seq")
+ (version (string-append "1.1-" revision "." commit))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/aboyle/F-seq.git")
+ (commit commit)))
+ (file-name (string-append name "-" version))
+ (sha256
+ (base32
+ "1nk33k0yajg2id4g59bc4szr58r2q6pdq42vgcw054m8ip9wv26h"))
+ (modules '((guix build utils)))
+ ;; Remove bundled Java library archives.
+ (snippet
+ '(begin
+ (for-each delete-file (find-files "lib" ".*"))
+ #t))))
+ (build-system ant-build-system)
+ (arguments
+ `(#:tests? #f ; no tests included
+ #:phases
+ (modify-phases %standard-phases
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((target (assoc-ref outputs "out"))
+ (doc (string-append target "/share/doc/f-seq/")))
+ (mkdir-p target)
+ (mkdir-p doc)
+ (substitute* "bin/linux/fseq"
+ (("java") (which "java")))
+ (install-file "README.txt" doc)
+ (install-file "bin/linux/fseq" (string-append target "/bin"))
+ (install-file "build~/fseq.jar" (string-append target "/lib"))
+ (copy-recursively "lib" (string-append target "/lib"))
+ #t))))))
+ (inputs
+ `(("perl" ,perl)
+ ("java-commons-cli" ,java-commons-cli)))
+ (home-page "http://fureylab.web.unc.edu/software/fseq/")
+ (synopsis "Feature density estimator for high-throughput sequence tags")
+ (description
+ "F-Seq is a software package that generates a continuous tag sequence
+density estimation allowing identification of biologically meaningful sites
+whose output can be displayed directly in the UCSC Genome Browser.")
+ (license license:gpl3+))))
--
2.13.0