gnu: Add velvet.
* gnu/packages/bioinformatics.scm (velvet): New variable.
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@ -14425,3 +14425,61 @@ datasets. A popular implementation of t-SNE uses the Barnes-Hut algorithm to
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approximate the gradient at each iteration of gradient descent. This package
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is a Cython wrapper for FIt-SNE.")
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(license license:bsd-4)))
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(define-public velvet
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(package
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(name "velvet")
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(version "1.2.10")
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(source (origin
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(method url-fetch)
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(uri (string-append "https://www.ebi.ac.uk/~zerbino/velvet/"
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"velvet_" version ".tgz"))
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(sha256
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(base32
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"0h3njwy66p6bx14r3ar1byb0ccaxmxka4c65rn4iybyiqa4d8kc8"))
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;; Delete bundled libraries
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(modules '((guix build utils)))
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(snippet
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'(begin
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(delete-file "Manual.pdf")
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(delete-file-recursively "third-party")
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#t))))
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(build-system gnu-build-system)
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(arguments
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`(#:make-flags '("OPENMP=t")
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#:test-target "test"
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#:phases
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(modify-phases %standard-phases
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(delete 'configure)
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(add-after 'unpack 'fix-zlib-include
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(lambda _
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(substitute* "src/binarySequences.c"
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(("../third-party/zlib-1.2.3/zlib.h") "zlib.h"))
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#t))
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(replace 'install
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(lambda* (#:key outputs #:allow-other-keys)
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(let* ((out (assoc-ref outputs "out"))
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(bin (string-append out "/bin"))
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(doc (string-append out "/share/doc/velvet")))
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(mkdir-p bin)
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(mkdir-p doc)
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(install-file "velveth" bin)
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(install-file "velvetg" bin)
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(install-file "Manual.pdf" doc)
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(install-file "Columbus_manual.pdf" doc)
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#t))))))
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(inputs
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`(("openmpi" ,openmpi)
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("zlib" ,zlib)))
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(native-inputs
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`(("texlive" ,(texlive-union (list texlive-latex-graphics
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texlive-latex-hyperref)))))
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(home-page "https://www.ebi.ac.uk/~zerbino/velvet/")
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(synopsis "Nucleic acid sequence assembler for very short reads")
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(description
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"Velvet is a de novo genomic assembler specially designed for short read
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sequencing technologies, such as Solexa or 454. Velvet currently takes in
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short read sequences, removes errors then produces high quality unique
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contigs. It then uses paired read information, if available, to retrieve the
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repeated areas between contigs.")
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(license license:gpl2+)))
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