gnu: Remove gess.

* gnu/packages/bioinformatics.scm (gess): Delete variable.
This commit is contained in:
Maxim Cournoyer 2022-04-29 23:31:00 -04:00
parent 75f49c4cc1
commit a5e29cd838
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@ -8984,72 +8984,6 @@ (define-public trim-galore
remove biased methylation positions for RRBS sequence files.") remove biased methylation positions for RRBS sequence files.")
(license license:gpl3+))) (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 (define-public phylip
(package (package
(name "phylip") (name "phylip")