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-rw-r--r--gnu/packages/bioinformatics.scm61
1 files changed, 61 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index fbff587302..2844c46075 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9328,3 +9328,64 @@ with narrow binding events such as transcription factor ChIP-seq.")
adapter trimming as well as quality control, with some added functionality to
remove biased methylation positions for RRBS sequence files.")
(license license:gpl3+)))
+
+(define-public gess
+ (package
+ (name "gess")
+ (version "1.0")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "http://compbio.uthscsa.edu/"
+ "GESS_Web/files/"
+ "gess-" version ".src.tar.gz"))
+ (sha256
+ (base32
+ "0hyk403kxscclzfs24pvdgiv0wm03kjcziqdrp5w46cb049gz0d7"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ; no tests
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (delete 'build)
+ (replace 'install
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let* ((python (assoc-ref inputs "python"))
+ (out (assoc-ref outputs "out"))
+ (bin (string-append out "/bin/"))
+ (target (string-append
+ out "/lib/python2.7/site-packages/gess/")))
+ (mkdir-p target)
+ (copy-recursively "." target)
+ ;; Make GESS.py executable
+ (chmod (string-append target "GESS.py") #o555)
+ ;; Add Python shebang to the top and make Matplotlib
+ ;; usable.
+ (substitute* (string-append target "GESS.py")
+ (("\"\"\"Description:" line)
+ (string-append "#!" (which "python") "
+import matplotlib
+matplotlib.use('Agg')
+" line)))
+ ;; Make sure GESS has all modules in its path
+ (wrap-program (string-append target "GESS.py")
+ `("PYTHONPATH" ":" prefix (,target ,(getenv "PYTHONPATH"))))
+ (mkdir-p bin)
+ (symlink (string-append target "GESS.py")
+ (string-append bin "GESS.py"))
+ #t))))))
+ (inputs
+ `(("python" ,python-2)
+ ("python2-pysam" ,python2-pysam)
+ ("python2-scipy" ,python2-scipy)
+ ("python2-numpy" ,python2-numpy)
+ ("python2-networkx" ,python2-networkx)
+ ("python2-biopython" ,python2-biopython)))
+ (home-page "http://compbio.uthscsa.edu/GESS_Web/")
+ (synopsis "Detect exon-skipping events from raw RNA-seq data")
+ (description
+ "GESS is an implementation of a novel computational method to detect de
+novo exon-skipping events directly from raw RNA-seq data without the prior
+knowledge of gene annotation information. GESS stands for the graph-based
+exon-skipping scanner detection scheme.")
+ (license license:bsd-3)))