From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from eggs.gnu.org ([2001:4830:134:3::10]:58703) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1e2lUV-00076f-2Q for guix-patches@gnu.org; Thu, 12 Oct 2017 17:58:08 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1e2lUQ-0006mp-TS for guix-patches@gnu.org; Thu, 12 Oct 2017 17:58:06 -0400 Received: from debbugs.gnu.org ([208.118.235.43]:56004) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1e2lUQ-0006ml-Qq for guix-patches@gnu.org; Thu, 12 Oct 2017 17:58:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1e2lUQ-0005wM-Jn for guix-patches@gnu.org; Thu, 12 Oct 2017 17:58:02 -0400 Subject: [bug#28802] [PATCH] gnu: Add paml. Resent-Message-ID: Received: from eggs.gnu.org ([2001:4830:134:3::10]:58562) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1e2lTX-000758-Pr for guix-patches@gnu.org; Thu, 12 Oct 2017 17:57:08 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1e2lTT-0006Nk-RR for guix-patches@gnu.org; Thu, 12 Oct 2017 17:57:07 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21117) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1e2lTT-0006NW-Ip for guix-patches@gnu.org; Thu, 12 Oct 2017 17:57:03 -0400 From: Ricardo Wurmus Date: Thu, 12 Oct 2017 23:56:32 +0200 Message-Id: <20171012215632.713-1-rekado@elephly.net> List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+kyle=kyleam.com@gnu.org Sender: "Guix-patches" To: 28802@debbugs.gnu.org Cc: Ricardo Wurmus From: Ricardo Wurmus * 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