From debbugs-submit-bounces@debbugs.gnu.org Thu Oct 12 17:57:17 2017 Received: (at submit) by debbugs.gnu.org; 12 Oct 2017 21:57:17 +0000 Received: from localhost ([127.0.0.1]:36452 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1e2lTh-0005vK-3r for submit@debbugs.gnu.org; Thu, 12 Oct 2017 17:57:17 -0400 Received: from eggs.gnu.org ([208.118.235.92]:39365) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1e2lTf-0005v7-9m for submit@debbugs.gnu.org; Thu, 12 Oct 2017 17:57:15 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1e2lTZ-0006QK-6r for submit@debbugs.gnu.org; Thu, 12 Oct 2017 17:57:10 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-0.5 required=5.0 tests=BAYES_05,T_DKIM_INVALID autolearn=disabled version=3.3.2 Received: from lists.gnu.org ([2001:4830:134:3::11]:47030) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1e2lTZ-0006QC-31 for submit@debbugs.gnu.org; Thu, 12 Oct 2017 17:57:09 -0400 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 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1507845396; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:To:Cc:Subject:Date:Message-Id; l=2142; bh=nsIqGnW/QTfkeXT8/Bb8G1fr/sz6Nxwiekgt7L+fZRU=; b=EG8BfsMgQDs5RUZM6xqjG038G7XoqP9Ubyr85FjWiUgrR9V7CTlJNPBAP8ydtqGb 3NdFCSuxYfHkVtfX0cXjrHe7zgLd445PXCmWDhR3ZlgnfgtG8xrLQgYuXhYVLH/txt+ m1bWCwfM9iUQuZFmvVTomNKtu9xWTnif0XKxk8sk= Received: from localhost (port-92-200-64-181.dynamic.qsc.de [92.200.64.181]) by mx.zohomail.com with SMTPS id 1507845396706962.1607250788516; Thu, 12 Oct 2017 14:56:36 -0700 (PDT) From: Ricardo Wurmus To: guix-patches@gnu.org Subject: [PATCH] gnu: Add paml. Date: Thu, 12 Oct 2017 23:56:32 +0200 Message-Id: <20171012215632.713-1-rekado@elephly.net> X-Mailer: git-send-email 2.14.1 X-ZohoMailClient: External X-detected-operating-system: by eggs.gnu.org: GNU/Linux 3.x [fuzzy] X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.6.x X-Received-From: 2001:4830:134:3::11 X-Spam-Score: -4.0 (----) X-Debbugs-Envelope-To: submit Cc: Ricardo Wurmus X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -4.0 (----) 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 From debbugs-submit-bounces@debbugs.gnu.org Fri Oct 13 04:51:18 2017 Received: (at 28802) by debbugs.gnu.org; 13 Oct 2017 08:51:18 +0000 Received: from localhost ([127.0.0.1]:36845 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1e2vgc-00077A-1M for submit@debbugs.gnu.org; Fri, 13 Oct 2017 04:51:18 -0400 Received: from hera.aquilenet.fr ([141.255.128.1]:52567) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1e2vga-000772-9S for 28802@debbugs.gnu.org; Fri, 13 Oct 2017 04:51:17 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id CB936DC67; Fri, 13 Oct 2017 10:51:16 +0200 (CEST) X-Virus-Scanned: Debian amavisd-new at aquilenet.fr Received: from hera.aquilenet.fr ([127.0.0.1]) by localhost (hera.aquilenet.fr [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id jFLLqFPegDSD; Fri, 13 Oct 2017 10:51:15 +0200 (CEST) Received: from ribbon (unknown [193.50.110.214]) by hera.aquilenet.fr (Postfix) with ESMTPSA id BF4EEDA66; Fri, 13 Oct 2017 10:51:15 +0200 (CEST) From: ludo@gnu.org (Ludovic =?utf-8?Q?Court=C3=A8s?=) To: Ricardo Wurmus Subject: Re: [bug#28802] [PATCH] gnu: Add paml. References: <20171012215632.713-1-rekado@elephly.net> X-URL: http://www.fdn.fr/~lcourtes/ X-Revolutionary-Date: 22 =?utf-8?Q?Vend=C3=A9miaire?= an 226 de la =?utf-8?Q?R=C3=A9volution?= X-PGP-Key-ID: 0x090B11993D9AEBB5 X-PGP-Key: http://www.fdn.fr/~lcourtes/ludovic.asc X-PGP-Fingerprint: 3CE4 6455 8A84 FDC6 9DB4 0CFB 090B 1199 3D9A EBB5 X-OS: x86_64-pc-linux-gnu Date: Fri, 13 Oct 2017 10:51:14 +0200 In-Reply-To: <20171012215632.713-1-rekado@elephly.net> (Ricardo Wurmus's message of "Thu, 12 Oct 2017 23:56:32 +0200") Message-ID: <878tgfqvlp.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/25.3 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain X-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: 28802 Cc: Ricardo Wurmus , 28802@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: 1.0 (+) Ricardo Wurmus skribis: > From: Ricardo Wurmus > > * gnu/packages/bioinformatics.scm (paml): New variable. LGTM, thanks! Ludo'. From debbugs-submit-bounces@debbugs.gnu.org Fri Oct 13 05:16:24 2017 Received: (at 28802-done) by debbugs.gnu.org; 13 Oct 2017 09:16:24 +0000 Received: from localhost ([127.0.0.1]:36874 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1e2w4u-0007tM-2E for submit@debbugs.gnu.org; Fri, 13 Oct 2017 05:16:24 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21087) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1e2w4s-0007tA-67 for 28802-done@debbugs.gnu.org; Fri, 13 Oct 2017 05:16:22 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1507886159; s=zoho; d=elephly.net; i=rekado@elephly.net; h=References:From:To:Subject:In-reply-to:Date:Message-ID:MIME-Version:Content-Type:Content-Transfer-Encoding; l=263; bh=IPfRQcVxjxx5FiTnDXR2kzJlM4tR13YfkkW5z5+KY44=; b=c+RQ2dhVLU7QTKWE9/xn/O9VyHiVFucuJaa6qaeG9EJ88k2I/136bplypUeq226J UC6V20vlhRjZCCwWe9bwZSPcXvBQEtgz0ZtDGVuT9bd3JvRcI6P5qhsS2Lia5xCWWTY R1V/1byn84BcoLCLgqSwE8BoDPH3loiDSzTCIhhE= Received: from localhost (141.80.247.77 [141.80.247.77]) by mx.zohomail.com with SMTPS id 1507886159280409.91878402094176; Fri, 13 Oct 2017 02:15:59 -0700 (PDT) References: <20171012215632.713-1-rekado@elephly.net> User-agent: mu4e 0.9.18; emacs 25.3.1 From: Ricardo Wurmus To: 28802-done@debbugs.gnu.org Subject: Re: [PATCH] gnu: Add paml. In-reply-to: <20171012215632.713-1-rekado@elephly.net> X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Date: Fri, 13 Oct 2017 11:15:56 +0200 Message-ID: <87y3offlwz.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-ZohoMailClient: External X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 28802-done X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -0.0 (/) > + (docs '("Bismark_User_Guide.pdf" > + "RELEASE_NOTES.txt"))) I removed this, because it is not used. “guix lint” does not complain, so I pushed it to master. -- Ricardo GPG: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC https://elephly.net From debbugs-submit-bounces@debbugs.gnu.org Fri Oct 13 05:23:20 2017 Received: (at 28802) by debbugs.gnu.org; 13 Oct 2017 09:23:20 +0000 Received: from localhost ([127.0.0.1]:36885 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1e2wBb-00086X-QA for submit@debbugs.gnu.org; Fri, 13 Oct 2017 05:23:19 -0400 Received: from mailhub2.soe.uq.edu.au ([130.102.132.209]:51688 helo=newmailhub.uq.edu.au) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1e2wBZ-00086I-A3 for 28802@debbugs.gnu.org; Fri, 13 Oct 2017 05:23:18 -0400 Received: from smtp1.soe.uq.edu.au (smtp1.soe.uq.edu.au [10.138.113.40]) by newmailhub.uq.edu.au (8.14.5/8.14.5) with ESMTP id v9D9NC86043976; Fri, 13 Oct 2017 19:23:13 +1000 Received: from [192.168.1.105] ([123.200.134.98]) (authenticated bits=0) by smtp1.soe.uq.edu.au (8.14.5/8.14.5) with ESMTP id v9D9NB2Q059215 (version=TLSv1.2 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT); Fri, 13 Oct 2017 19:23:12 +1000 Subject: Re: [bug#28802] [PATCH] gnu: Add paml. To: Ricardo Wurmus , 28802@debbugs.gnu.org References: <20171012215632.713-1-rekado@elephly.net> From: Ben Woodcroft Message-ID: <9e41021c-74e2-0642-3423-52df07f8b679@uq.edu.au> Date: Fri, 13 Oct 2017 19:23:11 +1000 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:52.0) Gecko/20100101 Thunderbird/52.3.0 MIME-Version: 1.0 In-Reply-To: <20171012215632.713-1-rekado@elephly.net> Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 7bit Content-Language: en-US X-UQ-FilterTime: 1507886595 X-Scanned-By: MIMEDefang 2.73 on UQ Mailhub X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 28802 Cc: Ricardo Wurmus X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -2.3 (--) Hi Ricardo, Thanks for the package. On 13/10/17 07:56, Ricardo Wurmus wrote: > + (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) Since you've already pushed I didn't test out this package, but I notice that the above line is superfluous (though harmless). ben From debbugs-submit-bounces@debbugs.gnu.org Fri Oct 13 05:37:11 2017 Received: (at 28802) by debbugs.gnu.org; 13 Oct 2017 09:37:11 +0000 Received: from localhost ([127.0.0.1]:36892 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1e2wP1-0008VH-0c for submit@debbugs.gnu.org; Fri, 13 Oct 2017 05:37:11 -0400 Received: from pegasus.bbbm.mdc-berlin.de ([141.80.25.20]:32854) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1e2wOz-0008V5-JW for 28802@debbugs.gnu.org; Fri, 13 Oct 2017 05:37:10 -0400 Received: from localhost (localhost [127.0.0.1]) by pegasus.bbbm.mdc-berlin.de (Postfix) with ESMTP id A556D42DE61; Fri, 13 Oct 2017 11:37:08 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-transfer-encoding:content-type:content-type:mime-version :message-id:date:date:in-reply-to:subject:subject:from:from :user-agent:references:received:received:received; s=mdc; t= 1507887423; x=1509701824; bh=at0z8XhfNmvfVpwrvff2fHENLxmRAfw9ghX 16+j77FI=; b=KzYkMAUsF/ihFYmiHdRxL1hV1GX/Qi/q2ydtSnp8YFM182JQB4T ugbFoCk7HqUJDEF2vEJmB1Dc87XfHSaomPV0PXVnxTnZv7EHRF4RxKAEo44Kna/T SvRwuZdTKsZc+zLjeVque8nznzUIUdoRnhigjy4EIHcMjJQoX1+fJWgk= X-Virus-Scanned: amavisd-new at mdc-berlin.de Received: from pegasus.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (pegasus.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id B_v0J6I-BdRk; Fri, 13 Oct 2017 11:37:03 +0200 (CEST) Received: from HTCAONE.mdc-berlin.net (puck.citx.mdc-berlin.de [141.80.36.101]) (using TLSv1 with cipher ECDHE-RSA-AES256-SHA (256/256 bits)) (No client certificate requested) by pegasus.bbbm.mdc-berlin.de (Postfix) with ESMTPS; Fri, 13 Oct 2017 11:37:03 +0200 (CEST) Received: from localhost (141.80.180.135) by HTCAONE.mdc-berlin.net (141.80.180.125) with Microsoft SMTP Server (TLS) id 14.3.361.1; Fri, 13 Oct 2017 11:35:02 +0200 References: <20171012215632.713-1-rekado@elephly.net> <9e41021c-74e2-0642-3423-52df07f8b679@uq.edu.au> User-agent: mu4e 0.9.18; emacs 25.2.1 From: Ricardo Wurmus To: Ben Woodcroft Subject: Re: [bug#28802] [PATCH] gnu: Add paml. In-Reply-To: <9e41021c-74e2-0642-3423-52df07f8b679@uq.edu.au> X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Date: Fri, 13 Oct 2017 11:35:02 +0200 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: 8bit X-Originating-IP: [141.80.180.135] X-TM-AS-Product-Ver: SMEX-11.0.0.4283-8.100.1062-23392.006 X-TM-AS-Result: No--4.905900-0.000000-31 X-TM-AS-MatchedID: 150567-139010-700075-188198-702106-105040-709251-700040-7 00756-700272-703330-701298-700970-848362-701005-707062-106420-148004-148133 -10019-41000-42000-42003-63 X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-Spam-Score: -5.0 (-----) X-Debbugs-Envelope-To: 28802 Cc: 28802@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -5.0 (-----) Hi Ben, > On 13/10/17 07:56, Ricardo Wurmus wrote: >> + (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) > Since you've already pushed I didn't test out this package, but I notice > that the above line is superfluous (though harmless). I removed the “docs” definition before pushing. -- Ricardo From debbugs-submit-bounces@debbugs.gnu.org Fri Oct 13 06:23:12 2017 Received: (at 28802) by debbugs.gnu.org; 13 Oct 2017 10:23:12 +0000 Received: from localhost ([127.0.0.1]:36930 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1e2x7Y-0001Oe-Ev for submit@debbugs.gnu.org; Fri, 13 Oct 2017 06:23:12 -0400 Received: from eggs.gnu.org ([208.118.235.92]:37398) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1e2x7X-0001ON-1L for 28802@debbugs.gnu.org; Fri, 13 Oct 2017 06:23:11 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1e2x7N-0007Gu-JQ for 28802@debbugs.gnu.org; Fri, 13 Oct 2017 06:23:05 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-0.0 required=5.0 tests=BAYES_20,RP_MATCHES_RCVD autolearn=disabled version=3.3.2 Received: from fencepost.gnu.org ([2001:4830:134:3::e]:39705) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1e2x73-0006xA-3I; Fri, 13 Oct 2017 06:22:41 -0400 Received: from ip-80-113-14-101.ip.prioritytelecom.net ([80.113.14.101]:37291 helo=yellowstone) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1e2x72-0001K2-Jp; Fri, 13 Oct 2017 06:22:40 -0400 References: <20171012215632.713-1-rekado@elephly.net> User-agent: mu4e 0.9.18; emacs 25.1.1 From: Roel Janssen To: Ricardo Wurmus Subject: Re: [bug#28802] [PATCH] gnu: Add paml. Message-ID: <87bmlb4abu.fsf@gnu.org> In-reply-to: <20171012215632.713-1-rekado@elephly.net> Date: Fri, 13 Oct 2017 12:22:32 +0200 MIME-Version: 1.0 Content-Type: text/plain X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 2001:4830:134:3::e X-Spam-Score: -5.0 (-----) X-Debbugs-Envelope-To: 28802 Cc: Ricardo Wurmus , 28802@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -5.0 (-----) Ricardo Wurmus writes: > 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))) I guess I'm too late already. I had a similar patch, but the program uses the data files it ships with, and expects them to be in the same location. So this patch seems incomplete to me. Anyway.. it has already been pushed. Kind regards, Roel Janssen From debbugs-submit-bounces@debbugs.gnu.org Fri Oct 13 09:25:46 2017 Received: (at 28802) by debbugs.gnu.org; 13 Oct 2017 13:25:46 +0000 Received: from localhost ([127.0.0.1]:36999 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1e2zyE-0000do-9J for submit@debbugs.gnu.org; Fri, 13 Oct 2017 09:25:46 -0400 Received: from sinope02.bbbm.mdc-berlin.de ([141.80.25.24]:55918) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1e2zyC-0000dc-ED for 28802@debbugs.gnu.org; Fri, 13 Oct 2017 09:25:45 -0400 Received: from localhost (localhost [127.0.0.1]) by sinope02.bbbm.mdc-berlin.de (Postfix) with ESMTP id C9ECBCDB0D4; Fri, 13 Oct 2017 15:25:41 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-transfer-encoding:content-type:content-type:mime-version :message-id:date:date:in-reply-to:subject:subject:from:from :user-agent:references:received:received:received; s=mdc; t= 1507901136; x=1509715537; bh=FSZ2X5+laydHN9lMWHa2Y+N+EAVb3biFQra Ja3rejSU=; b=GTX9Yns+T6MIaWtFOvSXSpfhFmbTE/gTOUsg5RKDacl1EpYEDOj mSEwG0vswYhB8ce2jvAZIhmr466oe4Os3/HhN18Gp0NySyGLBCKWwcGj4rhciDuh oXsbkt1nx3SKA2PSfvCKtvM1l2oKUbvzRSi4X2B7XPKRKQWKTmiuIo+8= X-Virus-Scanned: amavisd-new at mdc-berlin.de Received: from sinope02.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (sinope02.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id qEg0B_OTPGDG; Fri, 13 Oct 2017 15:25:36 +0200 (CEST) Received: from HTCAONE.mdc-berlin.net (puck.citx.mdc-berlin.de [141.80.36.101]) (using TLSv1 with cipher ECDHE-RSA-AES256-SHA (256/256 bits)) (No client certificate requested) by sinope02.bbbm.mdc-berlin.de (Postfix) with ESMTPS; Fri, 13 Oct 2017 15:25:35 +0200 (CEST) Received: from localhost (141.80.180.135) by HTCAONE.mdc-berlin.net (141.80.180.125) with Microsoft SMTP Server (TLS) id 14.3.361.1; Fri, 13 Oct 2017 15:25:34 +0200 References: <20171012215632.713-1-rekado@elephly.net> <87bmlb4abu.fsf@gnu.org> User-agent: mu4e 0.9.18; emacs 25.2.1 From: Ricardo Wurmus To: Roel Janssen Subject: Re: [bug#28802] [PATCH] gnu: Add paml. In-Reply-To: <87bmlb4abu.fsf@gnu.org> X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Date: Fri, 13 Oct 2017 15:25:34 +0200 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: 8bit X-Originating-IP: [141.80.180.135] X-TM-AS-Product-Ver: SMEX-11.0.0.4283-8.100.1062-23392.007 X-TM-AS-Result: No--7.392100-0.000000-31 X-TM-AS-MatchedID: 150567-139010-706891-113681-862883-705927-701837-710307-7 00970-703712-702358-700373-705388-705098-705178-701927-700264-701558-710718 -700752-105700-704425-706561-701021-188198-709251-862673-188019-112090-7107 39-702106-105040-704034-701604-148004-148133-29997-42000-42003-63 X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 28802 Cc: Ricardo Wurmus , 28802@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: 0.0 (/) Hi Roel, > I guess I'm too late already. I had a similar patch, but the program > uses the data files it ships with, and expects them to be in the same > location. So this patch seems incomplete to me. Oh, that’s too bad. Do you have a test case we could use to verify that the tools work correctly after installation? It doesn’t seem to be easy to fix this, as variables in which file names are stored are size-restricted, and as they are copied around multiple times it is difficult to ensure that our patch wouldn’t break things. Here’s an untested draft of the new phases, but I suspect this would take a lot more work: --8<---------------cut here---------------start------------->8--- (modify-phases %standard-phases (replace 'configure (lambda _ (substitute* "src/BFdriver.c" (("/bin/bash") (which "bash"))) (let ((share (string-append (assoc-ref outputs "out") "/share/paml/"))) (substitute* "" (("aaRatefile = dat/jones.dat" (string-append "aaRatefile = " share "jones.dat")))) (substitute* '("src/yn00.c" "src/baseml.c" "src/basemlg.c" "src/pamp.c" "src/codeml.c" "src/mcmctree.c" "src/BFdriver.c") (("ctlf\\[...?\\] ?= ?\"(yn00|pamp|baseml|codeml|mcmctree).ctl\"" _ file) (string-append "ctlf[PATH_MAX]=\"" share file ".ctl\""))) (substitute* "src/codeml.c" (("strcpy\\(com.daafile, \"jones.dat\"\\)") (string-append "strcpy(com.daafile, \"" share "jones.dat\")"))) (substitute* "src/evolver.c" (("char \\*MCctlf0\\[\\]=\\{\"MCbase.dat\",\"MCcodon.dat\",\"MCaa.dat\"\\}") (string-append "char *MCctlf0[]={" (string-join (map (lambda (f) (string-append "\"" share f "\"")) '("MCbase.dat" "MCcodon.dat" "MCaa.dat")) ",") "}")))) (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")) (share (string-append (assoc-ref outputs "out") "/share/paml")) (data (append (find-files ".." "\\.(ctl|dat)$") (find-files "../dat" "\\.dat$")))) (mkdir-p bin) (for-each (lambda (file) (install-file file bin)) tools) (for-each (lambda (file) (install-file file share)) data) (copy-recursively "../doc" docdir) #t)))) --8<---------------cut here---------------end--------------->8--- The alternative is to just install the data files to $out/share/paml and expect users to copy them to their current working directory. That seems to work. I prefer this over patching the code, which is much too invasive. What do you think? -- Ricardo From unknown Mon Aug 18 14:26:16 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Sat, 11 Nov 2017 12:24:04 +0000 User-Agent: Fakemail v42.6.9 # This is a fake control message. # # The action: # bug archived. thanks # This fakemail brought to you by your local debbugs # administrator