debian/0000755000000000000000000000000012164243075007172 5ustar debian/control0000644000000000000000000000204112164241051010562 0ustar Source: rnahybrid Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille Section: science Priority: optional Build-Depends: debhelper (>= 9), autotools-dev, libg2-dev Standards-Version: 3.9.4 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/rnahybrid/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/rnahybrid/trunk/ Homepage: http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/submission.html Package: rnahybrid Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Description: Fast and effective prediction of microRNA/target duplexes RNAhybrid is a tool for finding the minimum free energy hybridisation of a long and a short RNA. The hybridisation is performed in a kind of domain mode, ie. The short sequence is hybridised to the best fitting part of the long one. The tool is primarily meant as a means for microRNA target prediction. debian/rules0000755000000000000000000000165211735673716010272 0ustar #!/usr/bin/make -f # -*- makefile -*- %: dh $@ --with autotools_dev override_dh_auto_configure: dh_auto_configure -- --host=$(DEB_HOST_GNU_TYPE) \ --build=$(DEB_BUILD_GNU_TYPE) \ --prefix=/usr \ --mandir=\$${prefix}/share/man \ CFLAGS="$(CFLAGS)" \ LDFLAGS="-Wl,-z,defs" override_dh_auto_test: src/RNAhybrid -s 3utr_worm -t examples/cel-hbl-1.fasta -q examples/cel-let-7.fasta src/RNAcalibrate -d examples/3UTR_worm.freq -k 50 -l 50,30 -q examples/cel-let-7.fasta src/RNAhybrid -d 1.9,0.28 -t examples/cel-hbl-1.fasta -q examples/cel-let-7.fasta src/RNAhybrid -f 2,7 -d 1.9,0.28 -t examples/cel-hbl-1.fasta -q examples/cel-let-7.fasta src/RNAcalibrate -f 2,7 -d examples/3UTR_worm.freq -k 50 -l 50,30 -q examples/cel-let-7.fasta src/RNAhybrid -s 3utr_worm -t examples/cbr-hbl-1.fasta -q examples/cel-let-7.fasta -src/RNAeffective -k 30 -s -t examples/hbl-1.fasta -q examples/cel-let-7.fasta debian/examples0000644000000000000000000000001311735673114010731 0ustar examples/* debian/watch0000644000000000000000000000151111744327113010220 0ustar # version=3 # http://bibiserv.techfak.uni-bielefeld.de/download/tools/rnahybrid.html RNAhybrid-(.*)-src\.tar\.gz # # Watch file can not work - see: # -> http://lists.debian.org/debian-mentors/2012/04/msg00320.html # # Checked out with upstream and got answer: # # Date: Fri, 20 Apr 2012 15:36:37 +0200 # From: Jan Krueger # To: Andreas Tille # CC: Marc Rehmsmeier , bibi-help@cebitec.uni-bielefeld.de # Subject: Re: Please provide more simple download option for RNAhybrid source tarball # # Hi Andreas, # # the upcoming next version of bibiserv (called bibiserv2) # support direct links on the download page. # # The BiBiServ2 is currently in Beta test stage and will replace # the old BiBiServ somewhere in summer/autumn. debian/upstream0000644000000000000000000000106411752037023010752 0ustar Homepage: http://bibiserv.techfak.uni-bielefeld.de/rnahybrid Name: RNAhybrid Reference: author: Marc Rehmsmeier and Peter Steffen and Matthias Höchsmann and Robert Giegerich title: Fast and effective prediction of microRNA/target duplexes journal: RNA volume: 10 number: 10 pages: 1507-1517 year: 2004 PMID: 15383676 DOI: 10.1261/rna.5248604 URL: http://rnajournal.cshlp.org/content/10/10/1507.abstract eprint: http://rnajournal.cshlp.org/content/10/10/1507.full.pdf+html Webservice: http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/submission.html debian/copyright0000644000000000000000000000463311735677521011145 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: RNAhybrid Upstream-Contact: Marc Rehmsmeier Peter Steffen Matthias Hoechsmann Source: http://bibiserv.techfak.uni-bielefeld.de/download/tools/rnahybrid.html Files: * Copyright: 2004 Marc Rehmsmeier, Peter Steffen, Matthias Hoechsmann. License: GPL-2+ Files: mt19937-1.c Copyright: 1997, 1999 Makoto Matsumoto and Takuji Nishimura. License: LGPL-2+ This library is free software; you can redistribute it and/or modify it under the terms of the GNU Library General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. . This library 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 Library General Public License for more details. . You should have received a copy of the GNU Library General Public License along with this library; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA . On Debian systems, the complete text of the GNU Library General Public License can be found in `/usr/share/common-licenses/LGPL-2'. Files: debian/* Copyright: 2007 Charles Pless 2012 Andreas Tille License: GPL-2+ License: GPL-2+ This package 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. . This package 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 package; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA . On Debian systems, the complete text of the GNU General Public License can be found in `/usr/share/common-licenses/GPL'. debian/source/0000755000000000000000000000000011735670576010507 5ustar debian/source/format0000644000000000000000000000001411301174376011677 0ustar 3.0 (quilt) debian/changelog0000644000000000000000000000316312164243002011035 0ustar rnahybrid (2.1.1-2) unstable; urgency=low * debian/upstream: Make author field BibTeX compliant * debian/control: - cme fix dpkg-control - use anonscm in VCS fields * debian/patches/gcc-4.8.patch: Fix build error with gcc-4.8 by adding string.h Closes: #701348 -- Andreas Tille Mon, 01 Jul 2013 11:03:39 +0200 rnahybrid (2.1.1-1) unstable; urgency=low * New upstream version * debian/upstream: Remove duplicated entry for doi * debian/watch: Document why watch file can not work and what upstream has answered * debian/control: Fixed Vcs fields -- Andreas Tille Thu, 19 Apr 2012 08:21:18 +0200 rnahybrid (2.1-3) unstable; urgency=low [ Charles Plessy ] * Documented information in debian/upstream * Removed mention of the bibliographic reference in debian/control [ Andreas Tille ] * debian/source/format: 3.0 (quilt) * debian/control: Standards-Version: 3.9.3 (no changes needed) * debhelper 9 (control+compat) * debian/rules: short dh * debian/copyright: DEP5, verified using cme fix dpkg-copyright -- Andreas Tille Sat, 31 Mar 2012 22:52:18 +0200 rnahybrid (2.1-2) unstable; urgency=low [ Charles Plessy ] * Moved the Homepage: field out from the package's description. * Updated my email address. [ Andreas Tille ] * Standards-Version: 3.8.1 (no changes needed) -- Andreas Tille Mon, 01 Jun 2009 23:01:47 +0200 rnahybrid (2.1-1) unstable; urgency=low * Initial release (Closes: #426957) -- Charles Plessy Sun, 02 Sep 2007 11:03:35 +0900 debian/patches/0000755000000000000000000000000012164241354010617 5ustar debian/patches/gcc-4.8.patch0000644000000000000000000000065612164241354012712 0ustar Author: Andreas Tille BugClosed: http://bugs.debian.org/701348 LastChanged: Mon, 07 May 2012 23:26:52 +0200 Description: Fix build error with gcc-4.8 by adding string.h --- a/src/rnaeffective.c +++ b/src/rnaeffective.c @@ -17,6 +17,7 @@ #include #include #include +#include static char const rcsid[] = "$Id: rnaeffective.c,v 1.6 2004/11/16 15:41:12 marc Exp $"; debian/patches/series0000644000000000000000000000001612164240030012017 0ustar gcc-4.8.patch debian/compat0000644000000000000000000000000211735674113010374 0ustar 9 debian/docs0000644000000000000000000000000711735673104010045 0ustar README