From: Ricardo Wurmus <rekado@elephly.net>
To: 28802@debbugs.gnu.org
Cc: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Subject: [bug#28802] [PATCH] gnu: Add paml.
Date: Thu, 12 Oct 2017 23:56:32 +0200 [thread overview]
Message-ID: <20171012215632.713-1-rekado@elephly.net> (raw)
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
* gnu/packages/bioinformatics.scm (paml): New variable.
---
gnu/packages/bioinformatics.scm | 50 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 50 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 9a47b076c..2de57d447 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10085,3 +10085,53 @@ straight away. Its main features are:
and CHH context
@end itemize\n")
(license license:gpl3+)))
+
+(define-public paml
+ (package
+ (name "paml")
+ (version "4.9e")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "http://abacus.gene.ucl.ac.uk/software/"
+ "paml" version ".tgz"))
+ (sha256
+ (base32
+ "13zf6h9fiqghwhch2h06x1zdr6s42plsnqahflp5g7myr3han3s6"))
+ (modules '((guix build utils)))
+ ;; Remove Windows binaries
+ (snippet
+ '(begin
+ (for-each delete-file (find-files "." "\\.exe$"))
+ #t))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ; there are no tests
+ #:make-flags '("CC=gcc")
+ #:phases
+ (modify-phases %standard-phases
+ (replace 'configure
+ (lambda _
+ (substitute* "src/BFdriver.c"
+ (("/bin/bash") (which "bash")))
+ (chdir "src")
+ #t))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((tools '("baseml" "basemlg" "codeml"
+ "pamp" "evolver" "yn00" "chi2"))
+ (bin (string-append (assoc-ref outputs "out") "/bin"))
+ (docdir (string-append (assoc-ref outputs "out")
+ "/share/doc/paml"))
+ (docs '("Bismark_User_Guide.pdf"
+ "RELEASE_NOTES.txt")))
+ (mkdir-p bin)
+ (for-each (lambda (file) (install-file file bin)) tools)
+ (copy-recursively "../doc" docdir)
+ #t))))))
+ (home-page "http://abacus.gene.ucl.ac.uk/software/paml.html")
+ (synopsis "Phylogentic analysis by maximum likelihood")
+ (description "PAML (for Phylogentic Analysis by Maximum Likelihood)
+contains a few programs for model fitting and phylogenetic tree reconstruction
+using nucleotide or amino-acid sequence data.")
+ ;; GPLv3 only
+ (license license:gpl3)))
--
2.14.1
next reply other threads:[~2017-10-12 21:58 UTC|newest]
Thread overview: 7+ messages / expand[flat|nested] mbox.gz Atom feed top
2017-10-12 21:56 Ricardo Wurmus [this message]
2017-10-13 8:51 ` [bug#28802] [PATCH] gnu: Add paml Ludovic Courtès
2017-10-13 9:15 ` bug#28802: " Ricardo Wurmus
2017-10-13 9:23 ` [bug#28802] " Ben Woodcroft
2017-10-13 9:35 ` Ricardo Wurmus
2017-10-13 10:22 ` Roel Janssen
2017-10-13 13:25 ` Ricardo Wurmus
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