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gnu: Remove gess.
* gnu/packages/bioinformatics.scm (gess): Delete variable.
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@ -8984,72 +8984,6 @@ (define-public trim-galore
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remove biased methylation positions for RRBS sequence files.")
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(license license:gpl3+)))
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(define-public gess
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(package
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(name "gess")
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(version "1.0")
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(source (origin
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(method url-fetch)
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(uri (string-append "http://compbio.uthscsa.edu/"
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"GESS_Web/files/"
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"gess-" version ".src.tar.gz"))
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(sha256
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(base32
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"0hyk403kxscclzfs24pvdgiv0wm03kjcziqdrp5w46cb049gz0d7"))))
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(build-system gnu-build-system)
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(arguments
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`(#:tests? #f ; no tests
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#:phases
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(modify-phases %standard-phases
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(delete 'configure)
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(delete 'build)
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(replace 'install
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(lambda* (#:key inputs outputs #:allow-other-keys)
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(let* ((python (assoc-ref inputs "python"))
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(out (assoc-ref outputs "out"))
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(bin (string-append out "/bin/"))
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(target (string-append
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out "/lib/python"
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,(version-major+minor
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(package-version python))
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"/site-packages/gess/")))
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(mkdir-p target)
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(copy-recursively "." target)
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;; Make GESS.py executable
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(chmod (string-append target "GESS.py") #o555)
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;; Add Python shebang to the top and make Matplotlib
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;; usable.
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(substitute* (string-append target "GESS.py")
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(("\"\"\"Description:" line)
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(string-append "#!" (which "python") "
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import matplotlib
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matplotlib.use('Agg')
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" line)))
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;; Make sure GESS has all modules in its path
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(wrap-script (string-append target "GESS.py")
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#:guile (search-input-file inputs "bin/guile")
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`("GUIX_PYTHONPATH" ":" = (,target ,(getenv "GUIX_PYTHONPATH"))))
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(mkdir-p bin)
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(symlink (string-append target "GESS.py")
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(string-append bin "GESS.py"))
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#t))))))
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(inputs
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`(("python" ,python-2)
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("python2-pysam" ,python2-pysam)
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("python2-scipy" ,python2-scipy)
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("python2-numpy" ,python2-numpy)
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("python2-networkx" ,python2-networkx)
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("python2-biopython" ,python2-biopython)
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("guile" ,guile-3.0))) ; for the script wrapper
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(home-page "https://compbio.uthscsa.edu/GESS_Web/")
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(synopsis "Detect exon-skipping events from raw RNA-seq data")
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(description
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"GESS is an implementation of a novel computational method to detect de
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novo exon-skipping events directly from raw RNA-seq data without the prior
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knowledge of gene annotation information. GESS stands for the graph-based
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exon-skipping scanner detection scheme.")
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(license license:bsd-3)))
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(define-public phylip
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(package
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(name "phylip")
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