From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ben Woodcroft Subject: Re: [PATCH] tar bombs and muscle Date: Sun, 24 Apr 2016 10:04:01 +1000 Message-ID: <571C0D71.5000209@uq.edu.au> References: <569AEE9B.6070709@uq.edu.au> <20160116222954.6ae74288@openmailbox.org> Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="------------080506070300000409000407" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:36454) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1au7XA-0001du-3f for guix-devel@gnu.org; Sat, 23 Apr 2016 20:04:21 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1au7X5-00074e-45 for guix-devel@gnu.org; Sat, 23 Apr 2016 20:04:20 -0400 Received: from mailhub1.soe.uq.edu.au ([130.102.132.208]:34788 helo=newmailhub.uq.edu.au) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1au7X4-00074O-H3 for guix-devel@gnu.org; Sat, 23 Apr 2016 20:04:15 -0400 In-Reply-To: <20160116222954.6ae74288@openmailbox.org> List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: "Guix-devel" To: Eric Bavier Cc: "guix-devel@gnu.org" , Mathieu Lirzin This is a multi-part message in MIME format. --------------080506070300000409000407 Content-Type: text/plain; charset=windows-1252; format=flowed Content-Transfer-Encoding: 7bit On 17/01/16 14:29, Eric Bavier wrote: > On Sun, 17 Jan 2016 11:30:03 +1000 > Ben Woodcroft wrote: > >> There is a somewhat popular bioinformatics program muscle whose download >> tgz is a tar bomb. The bomb moniker seems especially appropriate here, >> since it made the gnu-build-system error out, and patching >> gnu-build-system requires a lot of rebuilding. In the attached patches I >> fixed gnu-build-system so that the "chdir" is omitted when there is no >> directory to chdir into, and then added muscle itself. > See https://lists.gnu.org/archive/html/guix-devel/2016-01/msg00165.html > > I think it might be what you're looking for. Now that url-fetch/tarbomb is available for general use, I've updated this patch and added a trivial test case. Thanks in advance for review. ben --------------080506070300000409000407 Content-Type: text/x-patch; name="0001-gnu-Add-muscle.patch" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="0001-gnu-Add-muscle.patch" >From 014be68f9e82847761f47f0363fa106bf708f14c Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Sat, 16 Jan 2016 22:12:23 +1000 Subject: [PATCH] gnu: Add muscle. * gnu/packages/bioinformatics.scm (muscle): New variable. --- gnu/packages/bioinformatics.scm | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 899ce1c..6e51dde 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2548,6 +2548,40 @@ RNA-Seq, the MISO model uses Bayesian inference to compute the probability that a read originated from a particular isoform.") (license license:gpl2))) +(define-public muscle + (package + (name "muscle") + (version "3.8.1551") + (source (origin + (method url-fetch/tarbomb) + (file-name (string-append name "-" version ".tar.gz")) + (uri (string-append + "http://www.drive5.com/muscle/muscle_src_" + version ".tar.gz")) + (sha256 + (base32 + "0bj8kj7sdizy3987zx6w7axihk40fk8rn76mpbqqjcnd64i5a367")))) + (build-system gnu-build-system) + (arguments + `(#:make-flags (list "LDLIBS = -lm") + #:phases + (modify-phases %standard-phases + (delete 'configure) + (replace 'check + ;; There are no tests, so just test if it runs. + (lambda _ (zero? (system* "./muscle" "-version")))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin"))) + (install-file "muscle" bin))))))) + (home-page "http://www.drive5.com/muscle") + (synopsis "Multiple sequence alignment program") + (description + "MUSCLE aims to be a fast and accurate multiple sequence alignment +program for nucleotide and protein sequences.") + (license license:public-domain))) + (define-public orfm (package (name "orfm") -- 2.6.3 --------------080506070300000409000407--