From a5e29cd838f8c4e0cbe8de79a5205def563ef579 Mon Sep 17 00:00:00 2001
From: Maxim Cournoyer <maxim.cournoyer@gmail.com>
Date: Fri, 29 Apr 2022 23:31:00 -0400
Subject: gnu: Remove gess.

* gnu/packages/bioinformatics.scm (gess): Delete variable.
---
 gnu/packages/bioinformatics.scm | 66 -----------------------------------------
 1 file changed, 66 deletions(-)

(limited to 'gnu')

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 @@ 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/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")
-- 
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