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| author | Ben Woodcroft <donttrustben@gmail.com> | 2016-07-12 16:04:02 +1000 |
|---|---|---|
| committer | Ben Woodcroft <donttrustben@gmail.com> | 2016-08-08 22:08:17 +1000 |
| commit | db7a344427637795b08728f4d5cdd6857682826d (patch) | |
| tree | 762a60f6bfa17808d0d7d83633e02aef24ef9243 /gnu/packages/bioinformatics.scm | |
| parent | 159a70167883b0b4d5237b7ef3493b54356f362e (diff) | |
| download | patches-db7a344427637795b08728f4d5cdd6857682826d.tar patches-db7a344427637795b08728f4d5cdd6857682826d.tar.gz | |
gnu: Add bppsuite.
* gnu/packages/bioinformatics.scm (bppsuite): New variable.
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 42 |
1 files changed, 42 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 78347331dc..4450580199 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -52,12 +52,14 @@ #:use-module (gnu packages gcc) #:use-module (gnu packages gd) #:use-module (gnu packages gtk) + #:use-module (gnu packages groff) #:use-module (gnu packages image) #:use-module (gnu packages imagemagick) #:use-module (gnu packages java) #:use-module (gnu packages linux) #:use-module (gnu packages logging) #:use-module (gnu packages machine-learning) + #:use-module (gnu packages man) #:use-module (gnu packages maths) #:use-module (gnu packages mpi) #:use-module (gnu packages ncurses) @@ -73,6 +75,7 @@ #:use-module (gnu packages statistics) #:use-module (gnu packages tbb) #:use-module (gnu packages tex) + #:use-module (gnu packages texinfo) #:use-module (gnu packages textutils) #:use-module (gnu packages time) #:use-module (gnu packages tls) @@ -659,6 +662,45 @@ analysis, phylogenetics, molecular evolution and population genetics. This library provides sequence-related modules.") (license license:cecill-c)))) +(define-public bppsuite + ;; The last release was in 2014 and the recommended way to install from source + ;; is to clone the git repository, so we do this. + ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page + (let ((commit "c516147f57aa50961121cd505bed52cd7603698b")) + (package + (name "bppsuite") + (version (string-append "2.2.0-1." (string-take commit 7))) + (source (origin + (method git-fetch) + (uri (git-reference + (url "http://biopp.univ-montp2.fr/git/bppsuite") + (commit commit))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 + "1y87pxvw0jxjizhq2dr9g2r91md45k1p9ih2sl1yy1y3p934l2kb")))) + (build-system cmake-build-system) + (arguments + `(#:parallel-build? #f + #:tests? #f)) ; There are no tests. + (native-inputs + `(("groff" ,groff) + ("man-db" ,man-db) + ("texinfo" ,texinfo))) + (inputs + `(("bpp-core" ,bpp-core) + ("bpp-seq" ,bpp-seq) + ("bpp-phyl" ,bpp-phyl) + ("bpp-phyl" ,bpp-popgen) + ("gcc" ,gcc-5))) + (home-page "http://biopp.univ-montp2.fr") + (synopsis "Bioinformatics tools written with the Bio++ libraries") + (description + "Bio++ is a set of C++ libraries for Bioinformatics, including sequence +analysis, phylogenetics, molecular evolution and population genetics. This +package provides command line tools using the Bio++ library.") + (license license:cecill-c)))) + (define-public blast+ (package (name "blast+") |