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| -rw-r--r-- | gnu/packages/bioinformatics.scm | 58 |
1 files changed, 58 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b9c1ecbcf3..23976ceda0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -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 is a Cython wrapper for FIt-SNE.") (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+))) |