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07/07: gnu: Add velvet.
From: |
guix-commits |
Subject: |
07/07: gnu: Add velvet. |
Date: |
Fri, 1 Mar 2019 06:55:46 -0500 (EST) |
rekado pushed a commit to branch master
in repository guix.
commit a27ca96f101f2e79931760a291ccedca97bb4303
Author: Ricardo Wurmus <address@hidden>
Date: Fri Mar 1 12:54:43 2019 +0100
gnu: Add velvet.
* gnu/packages/bioinformatics.scm (velvet): New variable.
---
gnu/packages/bioinformatics.scm | 58 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 58 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b9c1ecb..23976ce 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+)))
- branch master updated (7d14178 -> a27ca96), guix-commits, 2019/03/01
- 01/07: gnu: texlive-latex-hyperref: Add missing inputs., guix-commits, 2019/03/01
- 03/07: gnu: hypre: Remove indirect TexLive dependencies., guix-commits, 2019/03/01
- 02/07: gnu: texlive-latex-oberdiek: Add ifxetex to inputs., guix-commits, 2019/03/01
- 05/07: gnu: texlive-latex-pgf: Add missing input., guix-commits, 2019/03/01
- 06/07: gnu: discrover: Remove indirect TexLive dependencies., guix-commits, 2019/03/01
- 04/07: gnu: asymptote: Remove indirect TexLive dependency., guix-commits, 2019/03/01
- 07/07: gnu: Add velvet.,
guix-commits <=