debian/0000755000000000000000000000000012217720107007165 5ustar debian/infernal-doc.doc-base0000644000000000000000000000140711260422360013124 0ustar Document: infernal-doc Title: INFERNAL User’s Guide Author: Diana Kolbe, Eric Nawrocki, Sean Eddy Abstract: Sequence analysis using profiles of RNA secondary structure consensus Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence. Section: Science/Biology Format: pdf Files: /usr/share/doc/infernal/Userguide.pdf debian/README.source0000644000000000000000000000161411264001356011345 0ustar infernal - Changes to upstream source distribution ================================================== Upstream provides a readily readable userguide for Infernal, which is also available online at ftp://selab.janelia.org/pub/software/infernal/Userguide.pdf and should better not be distributed with the source to save disk space. The PDFs that are coming with the sources from which the userguide is built are indeed upstream's original sources. They are edited with a PDF editor. Upstream, Dr Eddy, was consulted in this issue. Some figures like the sequence alignments could be prepared with the infrastructure that Debian provides and thus would not be ultimately required to be shipped as PDFs. This is however tolerated. The redundancy of the squid folder with the Debian package biosquid needs to remain until upstream resolves the conflicts. -- Steffen Moeller Sun, 20 Jan 2008 23:05:22 +0100 debian/rules0000755000000000000000000000145212177710074010256 0ustar #!/usr/bin/make -f # -*- makefile -*- %: dh $@ override_dh_auto_clean: if [ -r Makefile ]; then $(MAKE) distclean; fi -cd documentation/userguide && if [ -r Makefile ]; then make distclean; fi -cd easel/documentation && if [ -r Makefile ]; then make distclean; fi dh_clean *.1 */*.log *.log */Makefile Makefile documentation/manpages/*.1 override_dh_compress : dh_compress -X.pdf override_dh_strip: dh_strip --dbg-package=infernal-dbg override_dh_auto_install: $(MAKE) install prefix=$(CURDIR)/debian/tmp override_dh_builddeb: dh_builddeb -- -Z xz get-orig-source: VERSION=`dpkg-parsechangelog | grep Ver | cut -d' ' -f2 | cut -d- -f1` ; \ URL="ftp://selab.janelia.org/pub/software/infernal/infernal-$${VERSION}.tar.gz"; \ ln -s infernal-$${VERSION}.tar.gz infernal_$${VERSION}.orig.tar.gz debian/patches/0000755000000000000000000000000012217720010010605 5ustar debian/patches/format_security.patch0000644000000000000000000000363111640376145015067 0ustar Index: infernal-1.0.2/easel/esl_getopts.c =================================================================== --- infernal-1.0.2.orig/easel/esl_getopts.c 2009-10-30 18:30:58.000000000 +0100 +++ infernal-1.0.2/easel/esl_getopts.c 2011-09-27 15:52:41.490289335 +0200 @@ -1270,7 +1270,7 @@ "Arg looks like option? Use %.24s%.24s if you really mean it.", g->opt[opti].name, *ret_optarg); } else - ESL_FAIL(eslESYNTAX, "Option %.24s requires an argument", g->opt[opti].name); + ESL_FAIL(eslESYNTAX, g->errbuf, "Option %.24s requires an argument", g->opt[opti].name); g->optstring = NULL; /* An optchar that takes an arg must terminate an optstring. */ } Index: infernal-1.0.2/easel/esl_msa.c =================================================================== --- infernal-1.0.2.orig/easel/esl_msa.c 2009-10-30 18:30:55.000000000 +0100 +++ infernal-1.0.2/easel/esl_msa.c 2011-09-27 15:57:44.961318373 +0200 @@ -3614,7 +3614,8 @@ ESL_MSA *msa = NULL; if (esl_tmpfile_named(tmpfile, &fp) != eslOK) goto ERROR; - fprintf(fp, s); + //fprintf(fp, s); // provokes error: format not a string literal and no format arguments [-Werror=format-security] + fputs(s,fp); fclose(fp); fp = NULL; if (esl_msafile_Open(tmpfile, fmt, NULL, &mfp) != eslOK) goto ERROR; Index: infernal-1.0.2/easel/esl_tree.c =================================================================== --- infernal-1.0.2.orig/easel/esl_tree.c 2009-10-30 18:30:58.000000000 +0100 +++ infernal-1.0.2/easel/esl_tree.c 2011-09-27 15:59:14.101032221 +0200 @@ -149,7 +149,8 @@ ESL_TREE *T = NULL; if (esl_tmpfile(tmpfile, &fp) != eslOK) goto ERROR; - fprintf(fp, s); + //fprintf(fp, s); // provokes error: format not a string literal and no format arguments [-Werror=format-security] + fputs(s,fp); rewind(fp); if (esl_tree_ReadNewick(fp, NULL, &T) != eslOK) goto ERROR; fclose(fp); debian/patches/series0000644000000000000000000000002712140544710012027 0ustar #format_security.patch debian/source/0000755000000000000000000000000012217720010010456 5ustar debian/source/format0000644000000000000000000000001412177674173011713 0ustar 3.0 (quilt) debian/copyright0000644000000000000000000001424112177710074011131 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Contact: Infernal developer team at HHMI Janelia Farm: Diana Kolbe Eric Nawrocki Sean Eddy . Source: ftp://infernal.janelia.org/pub/software/infernal Files: debian/* Copyright: © 2007-2008 Steffen Moeller © 2007-2008 Charles Plessy © 2009-2013 Andreas Tille License: GPL-3 Files: rigfilters/* Copyright: © 2004, Zasha Weinberg License: BSD-like Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: . - Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. - Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. - Neither the name of the University of Washington nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. . THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. Files: easel/esl_sse.c easel/esl_vmx.c Copyright: © 2007 Julien Pommier © 1992 Stephen Moshier License: BSD-Easel Files: easel/easel.c::esl_tmpfile() Copyright: © 1999-2001 David A. Wheeler License: BSD-Easel Files: easel/esl_regexp.c Copyright: © 1986, 1993, 1995 by University of Toronto License: BSD-Easel Files: easel/* Copyright: © 2004-2008 Sean R. Eddy © 2006-2008 Howard Hughes Medical Institute License: BSD-Easel License: BSD-Easel @EASEL_COPYRIGHT@ . The Easel library is freely modifiable and redistributable under the Janelia Farm Software License, a BSD license: . Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: . 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. . 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. . 3. Neither the name of the Howard Hughes Medical Institute nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. . THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, ANY IMPLIED WARRANTIES OF MERCHANTABILITY, NON-INFRINGEMENT, OR FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; REASONABLE ROYALTIES; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. Files: Userguide.pdf Copyright: Sean R. Eddy License: GPL-3 Comment: The PDFs that are coming with the sources from which the userguide is built are indeed upstream's original sources. They are edited with a PDF editor. Upstream, Dr Eddy, was consulted in this issue. Files: * Copyright: © 2001-2013 HHMI Janelia Farm © 1991-2013 Sean R. Eddy © 2005-2013 Eric P. Nawrocki © 2005-2011 Diana L. Kolbe © 2004 Zasha Weinberg © 1990 Don G. Gilbert © 1995-2006 Washington University in St. Louis © 1992-1995 Medical Research Council, UK © 2004 University of Washington, Seattle © 1986,1993,1995 University of Toronto © 1989-2001 Free Software Foundation © 1991 Massachusetts Institute of Technology License: GPL-3 License: GPL-3 This suite of programs is free software. You can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. . In other words, you may modify, copy, or redistribute this source code and its documentation, but if you do, you must preserve all these copyrights and distribute all derivative versions as free software under the GNU General Public License. . This software is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. . You should have received a copy of the GNU General Public License along with this software, in the file LICENSE; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301, USA or see http://www.gnu.org/ Comment: On Debian systems, the complete text of the GNU General Public License version 3 can be found in `/usr/share/common-licenses/GPL-3'. debian/infernal.install0000644000000000000000000000002412140544710012346 0ustar bin/* usr/bin debian/watch0000644000000000000000000000020612140544710010213 0ustar version=3 opts="passive,uversionmangle=s/(rc\d+)/~$1/" \ ftp://infernal.janelia.org/pub/software/infernal/infernal-([^-]*)\.tar\.gz debian/changelog0000644000000000000000000001014012217720001011024 0ustar infernal (1.1~rc4-2) unstable; urgency=low * Team upload. * Build-depends on libperl4-corelibs-perl (Closes: #724119). * debian/control: removed myself from Uploaders. -- Charles Plessy Mon, 23 Sep 2013 10:57:17 +0900 infernal (1.1~rc4-1) unstable; urgency=low * New upstream source * debian/source/format: 3.0 (quilt) * debian/control: - cme fix dpkg-control - debhelper 9 - do not Build-Depend: quilt since source format implies this - The package builds only on architectures with SSE instructions. Quoting from build log on armel: configure: WARNING: Infernal 1.1 requires VMX or SSE capability for parallel instructions. configure: error: It appears your platform has neither and will not support Infernal. So all non i386/amd64 architectures were excluded Closes: #718742 - use anonscm in Vcs fields * debian/rules: - remove redundant setting for flags which is handled by debhelper 9 automatically - use xz compression * debian/copyright: DEP5 -- Andreas Tille Mon, 05 Aug 2013 12:06:12 +0200 infernal (1.1~rc2-1) unstable; urgency=low * New upstream version - aiming to support RNAWorld BOINC project, with many thanks and regards to Yoyo! - cmscore no longer available * Bumped policy to 3.9.4 (no changes needed) - introduced hardening, with it build dep on dpkg-dev (>= 1.16.1~) -- Steffen Moeller Wed, 01 May 2013 20:24:17 +0200 infernal (1.0.2-3) UNRELEASED; urgency=low [ Steffen Moeller ] * Extra fixed for lintian cleanliness (Steffen) [ Andreas Tille ] * debian/upstream: - do not specify DOI twice - Moved PMID to references * debian/control: - Fixed Vcs-Svn field - Standards-Version: 3.9.3 (no changes needed) -- Andreas Tille Thu, 08 Mar 2012 11:44:54 +0100 infernal (1.0.2-2) unstable; urgency=low * Series of mall fixes (Closes: #643407). * source/format 3.0 * Policy to 3.9.2 * added infernal-dbg * corrected upstream's email address -- Steffen Moeller Tue, 27 Sep 2011 15:48:27 +0200 infernal (1.0.2-1) unstable; urgency=low * New upstream version -- Andreas Tille Tue, 03 Nov 2009 11:15:34 +0100 infernal (1.0-2) unstable; urgency=low * Switch to CDBS to benefit from automagical config.{sub,guess} update (debian/rules). Closes: #550253. * debian/control: - Depend on cdbs, downgraded requirement on debhelper from 7.1 to 7. - Transferred bibliographic information from the package description to debian/upstream-metadata.yaml. - Clarified the short description of the documentation package. * Removed debian/infernal.dirs, not needed. * Edited README.source, removing mention that infernal is in contrib. * debian/copyright points at the version 3 of the GPL. -- Charles Plessy Sat, 10 Oct 2009 11:22:35 +0900 infernal (1.0-1) unstable; urgency=low [ Charles Plessy ] * Updated my email address. [ Andreas Tille ] * New upstream version * debian/control: - Standards-Version: 3.8.3 (no changes needed) - Added myself to uploaders - s/Debian-Med/Debian Med/ - Build-Depends: debhelper (>= 7.1) autotools-dev - Package: infernal-doc * debian/rules rewritten to make use of short dh * debian/copyright: - added myself to Copyright holders of debian/* - squid is not part of the upstream tarball anymore so this paragraph was deleted - files/Userguide.pdf: Copied comment about PDF = source from README.Debian * debian/infernal-doc.doc-base * debian/infernal.install: install src/{trcyk,truncyk_check} to /usr/bin * TODO: Convince upstream to release libeazel which is also used in hmmer as a separate library instead of copying the code into different projects -- Andreas Tille Fri, 25 Sep 2009 15:17:22 +0200 infernal (0.81-1) experimental; urgency=low * Initial release (Closes: #441840) -- Steffen Moeller Mon, 10 Sep 2007 23:15:37 +0200 debian/infernal.manpages0000644000000000000000000000011412140544710012473 0ustar #documentation/manpages/* #share/man/man1/*.1 debian/tmp/share/man/man1/*.1 debian/upstream0000644000000000000000000000070711726107170010757 0ustar Homepage: http://infernal.janelia.org/ Reference: author: Nawrocki, Eric P. and Kolbe, Diana L. and Eddy, Sean R. title: "Infernal 1.0: inference of RNA alignments" journal: Bioinformatics volume: 25 number: 10 pages: 1335-1337 doi: 10.1093/bioinformatics/btp157 PMID: 19307242 year: 2009 URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/10/1335 eprint: http://bioinformatics.oxfordjournals.org/cgi/reprint/25/10/1335.pdf debian/control0000644000000000000000000000506412217717454010610 0ustar Source: infernal Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Andreas Tille Section: science Priority: optional Build-Depends: dpkg-dev (>= 1.16.1~), debhelper (>= 9), libperl4-corelibs-perl, autotools-dev Standards-Version: 3.9.4 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/infernal/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/infernal/trunk/ Homepage: http://infernal.janelia.org/ Package: infernal Architecture: i386 amd64 kfreebsd-i386 kfreebsd-amd64 hurd-i386 Depends: ${shlibs:Depends}, ${misc:Depends} Description: inference of RNA secondary structural alignments Infernal ("INFERence of RNA ALignment") searches DNA sequence databases for RNA structure and sequence similarities. It provides an implementation of a special variant of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence. . The tool is an integral component of the Rfam database. Package: infernal-doc Architecture: all Section: doc Depends: ${shlibs:Depends}, ${misc:Depends} Description: inference of RNA secondary structural alignments – documentation Infernal ("INFERence of RNA ALignment") searches DNA sequence databases for RNA structure and sequence similarities. It provides an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence. . This package provides the documentation which is shipped with the code of infernal. Package: infernal-dbg Architecture: i386 amd64 kfreebsd-i386 kfreebsd-amd64 hurd-i386 Section: debug Priority: extra Depends: ${misc:Depends}, infernal (= ${binary:Version}) Description: debug information for infernal This package contains extra information to help the debugging of the infernal suite. The package is auto-generated. You may be asked by the upstream developer to install it to help the identification of a technical problem. debian/README.Debian0000644000000000000000000000253711257724411011242 0ustar infernal for Debian ------------------- The documentation for easel contains many PDFs that are not buildable from source - although Debian most likely provide the tools at least to prepare some of the figures, e.g., a sequence alignment. Other figures would be more difficult to prepare. As an interim solution it was decided to leave that documentation out and users are requested to address the web pages of the upstream developers in this matter. The directory "squid" that is distributed with the source of infernal differs slightly from the biosquid Debian package. Upstream was contacted about this redundancy to his own software and the answer was to please leave with that situation since the two are not safely substituted for another. Infernal offers to be compiled for LAM-MPI. Please contact us if there is respective demand. Also, the Large File Support (LFS) was not activated, which may be of concern for large screening projects on files larger than 2GB. Infernal optionally uses the CFSQP library which is non-free. This is not supported by this Debian package. Please address the Userguide for instructions of a manual self-compilation and -installation. The packaging has become part of the Debian Med Blend and everyone interested is invited to join in for maintaining it. -- Steffen Moeller Mon, 10 Sep 2007 23:15:37 +0200 debian/compat0000644000000000000000000000000212177674411010376 0ustar 9 debian/infernal.docs0000644000000000000000000000002512140544710011631 0ustar README RELEASE-NOTES debian/infernal-doc.install0000644000000000000000000000004711257336502013124 0ustar Userguide.pdf usr/share/doc/infernal