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From: Ben Woodcroft <donttrustben@gmail.com>
To: guix-devel@gnu.org
Subject: [PATCH 14/22] gnu: Add bpp-core.
Date: Wed, 27 Jul 2016 22:54:15 +1000	[thread overview]
Message-ID: <2beb318e025e88bf0bb9d81f1a12c49c75c335b3.1469622379.git.donttrustben@gmail.com> (raw)
In-Reply-To: <20160727125423.7768-1-donttrustben@gmail.com>
In-Reply-To: <d3453a89a3858e7455e46040f96146f52b9c24aa.1469622378.git.donttrustben@gmail.com>

* gnu/packages/bioinformatics.scm (bpp-core): New variable.
---
 gnu/packages/bioinformatics.scm | 33 +++++++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 6065a00..4fb23a4 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -470,6 +470,39 @@ into separate processes; and more.")
     (inputs
      `(("python2-numpy" ,python2-numpy)))))
 
+(define-public bpp-core
+  ;; 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 "7d8bced0d1a87291ea8dd7046b7fb5ff9c35c582"))
+    (package
+      (name "bpp-core")
+      (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/bpp-core")
+                      (commit commit)))
+                (file-name (string-append name "-" version "-checkout"))
+                (sha256
+                 (base32
+                  "10djsq5vlnkilv436gnmh4irpk49v29pa69r6xiryg32xmvn909j"))))
+      (build-system cmake-build-system)
+      (arguments
+       `(#:parallel-build? #f))
+      (inputs
+       `(("gcc" ,gcc-5))) ; Compilation of bpp-phyl fails with GCC 4.9 so we
+                          ; compile all of the bpp packages with GCC 5.
+      (home-page "http://biopp.univ-montp2.fr")
+      (synopsis "C++ libraries for Bioinformatics")
+      (description
+       "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
+analysis, phylogenetics, molecular evolution and population genetics.  It is
+Object Oriented and is designed to be both easy to use and computer efficient.
+Bio++ intends to help programmers to write computer expensive programs, by
+providing them a set of re-usable tools.")
+      (license license:cecill-c))))
+
 (define-public blast+
   (package
     (name "blast+")
-- 
2.9.1

  parent reply	other threads:[~2016-07-27 12:55 UTC|newest]

Thread overview: 29+ messages / expand[flat|nested]  mbox.gz  Atom feed  top
2016-07-27 12:54 PATCH [0/22]: Add roary Ben Woodcroft
2016-07-27 12:54 ` [PATCH 01/22] gnu: parallel: Use full paths for executables Ben Woodcroft
2016-07-27 12:54   ` [PATCH 02/22] gnu: Add perl-xml-writer Ben Woodcroft
2016-07-27 12:54   ` [PATCH 03/22] gnu: Add perl-parse-yapp Ben Woodcroft
2016-07-27 12:54   ` [PATCH 04/22] gnu: Add perl-graph Ben Woodcroft
2016-07-27 12:54   ` [PATCH 05/22] gnu: Add perl-graph-readwrite Ben Woodcroft
2016-07-27 12:54   ` [PATCH 06/22] gnu: Add perl-log-log4perl Ben Woodcroft
2016-07-27 12:54   ` [PATCH 07/22] gnu: Add perl-file-slurper Ben Woodcroft
2016-07-27 12:54   ` [PATCH 08/22] gnu: Add perl-file-path Ben Woodcroft
2016-07-27 12:54   ` [PATCH 09/22] gnu: Add perl-file-grep Ben Woodcroft
2016-07-27 12:54   ` [PATCH 10/22] gnu: Add perl-array-utils Ben Woodcroft
2016-07-27 12:54   ` [PATCH 11/22] gnu: Add perl-test-files Ben Woodcroft
2016-07-27 12:54   ` [PATCH 12/22] gnu: Add perl-env-path Ben Woodcroft
2016-07-27 12:54   ` [PATCH 13/22] gnu: Add mcl Ben Woodcroft
2016-07-28 22:20     ` Leo Famulari
2016-07-27 12:54   ` Ben Woodcroft [this message]
2016-07-27 12:54   ` [PATCH 15/22] gnu: Add bpp-seq Ben Woodcroft
2016-07-27 12:54   ` [PATCH 16/22] gnu: Add bpp-phyl Ben Woodcroft
2016-07-27 12:54   ` [PATCH 17/22] gnu: Add bpp-popgen Ben Woodcroft
2016-07-27 12:54   ` [PATCH 18/22] gnu: Add bppsuite Ben Woodcroft
2016-07-27 12:54   ` [PATCH 19/22] gnu: Add exonerate Ben Woodcroft
2016-07-28 22:22     ` Leo Famulari
2016-07-27 12:54   ` [PATCH 20/22] gnu: Add prank Ben Woodcroft
2016-07-27 12:54   ` [PATCH 21/22] gnu: Add raxml Ben Woodcroft
2016-07-27 12:54   ` [PATCH 22/22] gnu: Add roary Ben Woodcroft
2016-07-29 21:07     ` Leo Famulari
2016-07-28 22:31   ` [PATCH 01/22] gnu: parallel: Use full paths for executables Leo Famulari
2016-07-31 11:26 ` PATCH [0/22]: Add roary Ludovic Courtès
2016-08-08 12:16   ` Ben Woodcroft

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