gnu: Add velvet.
* gnu/packages/bioinformatics.scm (velvet): New variable.
This commit is contained in:
parent
0ce256dc79
commit
a27ca96f10
|
@ -14425,3 +14425,61 @@ datasets. A popular implementation of t-SNE uses the Barnes-Hut algorithm to
|
||||||
approximate the gradient at each iteration of gradient descent. This package
|
approximate the gradient at each iteration of gradient descent. This package
|
||||||
is a Cython wrapper for FIt-SNE.")
|
is a Cython wrapper for FIt-SNE.")
|
||||||
(license license:bsd-4)))
|
(license license:bsd-4)))
|
||||||
|
|
||||||
|
(define-public velvet
|
||||||
|
(package
|
||||||
|
(name "velvet")
|
||||||
|
(version "1.2.10")
|
||||||
|
(source (origin
|
||||||
|
(method url-fetch)
|
||||||
|
(uri (string-append "https://www.ebi.ac.uk/~zerbino/velvet/"
|
||||||
|
"velvet_" version ".tgz"))
|
||||||
|
(sha256
|
||||||
|
(base32
|
||||||
|
"0h3njwy66p6bx14r3ar1byb0ccaxmxka4c65rn4iybyiqa4d8kc8"))
|
||||||
|
;; Delete bundled libraries
|
||||||
|
(modules '((guix build utils)))
|
||||||
|
(snippet
|
||||||
|
'(begin
|
||||||
|
(delete-file "Manual.pdf")
|
||||||
|
(delete-file-recursively "third-party")
|
||||||
|
#t))))
|
||||||
|
(build-system gnu-build-system)
|
||||||
|
(arguments
|
||||||
|
`(#:make-flags '("OPENMP=t")
|
||||||
|
#:test-target "test"
|
||||||
|
#:phases
|
||||||
|
(modify-phases %standard-phases
|
||||||
|
(delete 'configure)
|
||||||
|
(add-after 'unpack 'fix-zlib-include
|
||||||
|
(lambda _
|
||||||
|
(substitute* "src/binarySequences.c"
|
||||||
|
(("../third-party/zlib-1.2.3/zlib.h") "zlib.h"))
|
||||||
|
#t))
|
||||||
|
(replace 'install
|
||||||
|
(lambda* (#:key outputs #:allow-other-keys)
|
||||||
|
(let* ((out (assoc-ref outputs "out"))
|
||||||
|
(bin (string-append out "/bin"))
|
||||||
|
(doc (string-append out "/share/doc/velvet")))
|
||||||
|
(mkdir-p bin)
|
||||||
|
(mkdir-p doc)
|
||||||
|
(install-file "velveth" bin)
|
||||||
|
(install-file "velvetg" bin)
|
||||||
|
(install-file "Manual.pdf" doc)
|
||||||
|
(install-file "Columbus_manual.pdf" doc)
|
||||||
|
#t))))))
|
||||||
|
(inputs
|
||||||
|
`(("openmpi" ,openmpi)
|
||||||
|
("zlib" ,zlib)))
|
||||||
|
(native-inputs
|
||||||
|
`(("texlive" ,(texlive-union (list texlive-latex-graphics
|
||||||
|
texlive-latex-hyperref)))))
|
||||||
|
(home-page "https://www.ebi.ac.uk/~zerbino/velvet/")
|
||||||
|
(synopsis "Nucleic acid sequence assembler for very short reads")
|
||||||
|
(description
|
||||||
|
"Velvet is a de novo genomic assembler specially designed for short read
|
||||||
|
sequencing technologies, such as Solexa or 454. Velvet currently takes in
|
||||||
|
short read sequences, removes errors then produces high quality unique
|
||||||
|
contigs. It then uses paired read information, if available, to retrieve the
|
||||||
|
repeated areas between contigs.")
|
||||||
|
(license license:gpl2+)))
|
||||||
|
|
Loading…
Reference in New Issue