From: Ben Woodcroft <donttrustben@gmail.com>
To: guix-devel@gnu.org
Subject: [PATCH 21/22] gnu: Add raxml.
Date: Wed, 27 Jul 2016 22:54:22 +1000 [thread overview]
Message-ID: <b56734dd12a63a0e82985f364c8e45c11ebc482b.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 (raxml): New variable.
---
gnu/packages/bioinformatics.scm | 40 ++++++++++++++++++++++++++++++++++++++++
1 file changed, 40 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ea37a93..4e599a7 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3297,6 +3297,46 @@ format. It runs quickly, in an unsupervised fashion, handles gaps, handles
partial genes, and identifies translation initiation sites.")
(license license:gpl3+)))
+(define-public raxml
+ (package
+ (name "raxml")
+ (version "8.2.9")
+ (source
+ (origin
+ (method url-fetch)
+ (uri
+ (string-append
+ "https://github.com/stamatak/standard-RAxML/archive/v"
+ version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1pv8p2fy67y21a9y4cm7xpvxqjwz2v4201flfjshdq1p8j52rqf7"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ; There are no tests.
+ ;; Use 'standard' Makefile rather than SSE or AVX ones.
+ #:make-flags (list "-f" "Makefile.HYBRID.gcc")
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (bin (string-append out "/bin"))
+ (executable "raxmlHPC-HYBRID"))
+ (install-file executable bin)
+ (symlink (string-append bin "/" executable) "raxml"))
+ #t)))))
+ (inputs
+ `(("openmpi" ,openmpi)))
+ (home-page "http://sco.h-its.org/exelixis/web/software/raxml/index.html")
+ (synopsis "Randomized Axelerated Maximum Likelihood phylogenetic trees")
+ (description
+ "RAxML is a tool for phylogenetic analysis and post-analysis of large
+phylogenies.")
+ (license license:gpl2+)))
+
(define-public rsem
(package
(name "rsem")
--
2.9.1
next prev 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 ` [PATCH 14/22] gnu: Add bpp-core Ben Woodcroft
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 ` Ben Woodcroft [this message]
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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