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[PATCH 18/22] gnu: Add bppsuite.
From: |
Ben Woodcroft |
Subject: |
[PATCH 18/22] gnu: Add bppsuite. |
Date: |
Wed, 27 Jul 2016 22:54:19 +1000 |
* gnu/packages/bioinformatics.scm (bppsuite): New variable.
---
gnu/packages/bioinformatics.scm | 42 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 42 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 5dfc637..5ea2240 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -51,11 +51,13 @@
#:use-module (gnu packages gawk)
#:use-module (gnu packages gcc)
#:use-module (gnu packages gd)
+ #:use-module (gnu packages groff)
#:use-module (gnu packages image)
#: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)
@@ -70,6 +72,7 @@
#:use-module (gnu packages ruby)
#:use-module (gnu packages statistics)
#:use-module (gnu packages tbb)
+ #:use-module (gnu packages texinfo)
#:use-module (gnu packages textutils)
#:use-module (gnu packages time)
#:use-module (gnu packages tls)
@@ -607,6 +610,45 @@ 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+")
--
2.9.1
- [PATCH 09/22] gnu: Add perl-file-grep., (continued)
- [PATCH 09/22] gnu: Add perl-file-grep., Ben Woodcroft, 2016/07/27
- [PATCH 10/22] gnu: Add perl-array-utils., Ben Woodcroft, 2016/07/27
- [PATCH 11/22] gnu: Add perl-test-files., Ben Woodcroft, 2016/07/27
- [PATCH 12/22] gnu: Add perl-env-path., Ben Woodcroft, 2016/07/27
- [PATCH 13/22] gnu: Add mcl., Ben Woodcroft, 2016/07/27
- [PATCH 14/22] gnu: Add bpp-core., Ben Woodcroft, 2016/07/27
- [PATCH 15/22] gnu: Add bpp-seq., Ben Woodcroft, 2016/07/27
- [PATCH 16/22] gnu: Add bpp-phyl., Ben Woodcroft, 2016/07/27
- [PATCH 17/22] gnu: Add bpp-popgen., Ben Woodcroft, 2016/07/27
- [PATCH 18/22] gnu: Add bppsuite.,
Ben Woodcroft <=
- [PATCH 19/22] gnu: Add exonerate., Ben Woodcroft, 2016/07/27
- [PATCH 20/22] gnu: Add prank., Ben Woodcroft, 2016/07/27
- [PATCH 21/22] gnu: Add raxml., Ben Woodcroft, 2016/07/27
- [PATCH 22/22] gnu: Add roary., Ben Woodcroft, 2016/07/27
- Re: [PATCH 01/22] gnu: parallel: Use full paths for executables., Leo Famulari, 2016/07/28
- Re: PATCH [0/22]: Add roary., Ludovic Courtès, 2016/07/31