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| -rw-r--r-- | gnu/packages/bioinformatics.scm | 52 |
1 files changed, 52 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1dc39b8d23..3db67f5427 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9652,3 +9652,55 @@ 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 +such as transcription factor binding sites (ChIP-seq) or regions of open +chromatin (DNase-seq). Output can be displayed directly in the UCSC Genome +Browser.") + (license license:gpl3+)))) |