diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 40c060b2dc..32a9a8d526 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8984,72 +8984,6 @@ (define-public trim-galore 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/python" - ,(version-major+minor - (package-version python)) - "/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-script (string-append target "GESS.py") - #:guile (search-input-file inputs "bin/guile") - `("GUIX_PYTHONPATH" ":" = (,target ,(getenv "GUIX_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) - ("guile" ,guile-3.0))) ; for the script wrapper - (home-page "https://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))) - (define-public phylip (package (name "phylip")