debian/0000755000000000000000000000000012236247073007174 5ustar debian/watch0000644000000000000000000000006611110210467010212 0ustar version=3 http://sf.net/sibsim4/SIBsim4-(.*)\.tar\.gz debian/copyright0000644000000000000000000000271512236245666011142 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: SIBsim4 Upstream-Contact: Christian Iseli Source: http://sourceforge.net/projects/sibsim4/files/ Files: * Copyright: © 2001-2010 Christian Iseli , Claudio Lottaz Swiss Institute of Bioinformatics, and Ludwig Institute for Cancer Research (LICR) License: GPL2+ License: GPL2+ 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-2'. Files: debian/* Copyright: © 2007-2008 Nelson A. de Oliveira © 2010-2012 Andreas Tille License: GPL2+ debian/manpages0000644000000000000000000000001211110210467010666 0ustar SIBsim4.1 debian/changelog0000644000000000000000000000346112236247073011052 0ustar sibsim4 (0.20-2) unstable; urgency=low * debian/control: - cme fix dpkg-control - canonical Vcs URLs - debhelper 9 * debian/rules: cdbs -> dh * debian/README.Debian: Took over some information from debian/copyright which actually belongs here * debian/copyright: DEP5 * debian/patches/hardening.patch: Propagate hardening options -- Andreas Tille Tue, 05 Nov 2013 18:43:45 +0100 sibsim4 (0.20-1) unstable; urgency=low * New upstream version * Added myself to uploaders * Standards-Version: 3.8.4 (no changes needed) * Source-Format: 3.0 (quilt) * Debhalper 7 -- Andreas Tille Wed, 28 Apr 2010 16:58:04 +0200 sibsim4 (0.17-1) unstable; urgency=low * New upstream release. -- Nelson A. de Oliveira Sat, 17 May 2008 20:13:39 -0300 sibsim4 (0.16-1) unstable; urgency=low [ Charles Plessy ] * Moved the Homepage: field out from the package's description; * Updated Vcs-* fields in debian/control; * Added DM-Upload-Allowed. [ Nelson A. de Oliveira ] * New upstream release; * Updated Standards Version to 3.7.3; * Removed unused debian/patches. -- Nelson A. de Oliveira Tue, 18 Dec 2007 22:25:51 -0200 sibsim4 (0.15-2) unstable; urgency=low [ Nelson A. de Oliveira ] * I need to verify SVN before modifying a package... [ Charles Plessy ] * Add Subversion repository URL to debian/control. -- Nelson A. de Oliveira Sat, 28 Apr 2007 02:27:07 -0300 sibsim4 (0.15-1) unstable; urgency=low * New upstream release. -- Nelson A. de Oliveira Sat, 28 Apr 2007 02:16:34 -0300 sibsim4 (0.14-1) unstable; urgency=low * Initial release (Closes: #406286). -- Nelson A. de Oliveira Wed, 10 Jan 2007 02:13:20 -0200 debian/README.Debian0000644000000000000000000000223712236245531011236 0ustar SIBsim4 for Debian ================== The SIBsim4 project is based on sim4[1], which is a program designed to align an expressed DNA sequence with a genomic sequence, allowing for introns. Sim4 was written by Liliana Florea while working in Webb Miller's lab at the Pennsylvania State University. Here is the paper[2] describing sim4 (source code is also available). The name was chosen to denote the fact the SIBsim4 is a derivative work from sim4. SIB[3] stands for the Swiss Institute of Bioinformatics. Some code modifications were written by Claudio Lottaz, while working at SIB. SIBsim4 is currently developed and maintained by Christian Iseli, from the Ludwig Institute for Cancer Research LICR[4], Information Technology Office in Lausanne. LICR is a SIB partner. [1] http://globin.cse.psu.edu/html/docs/sim4.html [2] http://www.genome.org/cgi/content/full/8/9/967 L. Florea, G. Hartzell, Z. Zhang, G. Rubin, and W. Miller (1998) "A computer program for aligning a cDNA sequence with a genomic DNA sequence." Genome Research 8, 967-974. [3] http://www.isb-sib.ch/ [4] http://www.licr.org/ -- Andreas Tille Tue, 05 Nov 2013 18:43:45 +0100 debian/source/0000755000000000000000000000000011366046476010503 5ustar debian/source/format0000644000000000000000000000001411366046560011703 0ustar 3.0 (quilt) debian/compat0000644000000000000000000000000212236227172010370 0ustar 9 debian/install0000644000000000000000000000002011110210467010540 0ustar SIBsim4 usr/bin debian/patches/0000755000000000000000000000000012236246221010615 5ustar debian/patches/series0000644000000000000000000000002012236246036012026 0ustar hardening.patch debian/patches/hardening.patch0000644000000000000000000000121212236246221013571 0ustar Author: Andreas Tille LastChanged: Tue, 05 Nov 2013 18:43:45 +0100 Description: Propagate hardening options --- sibsim4-0.20.orig/Makefile +++ sibsim4-0.20/Makefile @@ -21,7 +21,7 @@ # to change it to this: # CFLAGS = -Xc -CFLAGS = -std=gnu99 -W -Wall -Wconversion -pedantic $(DEBUG) $(OPT) +CFLAGS += -std=gnu99 -W -Wall -Wconversion -pedantic $(DEBUG) $(OPT) # The default is GCC. On Solaris, you might put: @@ -42,7 +42,7 @@ OBJS = sim4b1.o align.o misc.o sim4.init.o sim4: $(OBJS) - $(CC) -o SIBsim4 $(CFLAGS) $(OBJS) $(LIBS) + $(CC) -o SIBsim4 $(CFLAGS) $(OBJS) $(LIBS) $(LDFLAGS) clean: rm -f SIBsim4 *.o debian/rules0000755000000000000000000000003612236243532010247 0ustar #!/usr/bin/make -f %: dh $@ debian/control0000644000000000000000000000212212236243550010570 0ustar Source: sibsim4 Maintainer: Debian Med Packaging Team Uploaders: Nelson A. de Oliveira , Andreas Tille Section: science Priority: optional Build-Depends: debhelper (>= 9) Standards-Version: 3.9.4 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/sibsim4/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/sibsim4/trunk/ Homepage: http://sibsim4.sourceforge.net/ Package: sibsim4 Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Description: align expressed RNA sequences on a DNA template The SIBsim4 project is based on sim4, which is a program designed to align an expressed DNA sequence with a genomic sequence, allowing for introns. SIBsim4 is a fairly extensive rewrite of the original code with the following goals: * speed improvement; * allow large, chromosome scale, DNA sequences to be used; * provide more detailed output about splice types; * provide more detailed output about polyA sites; * misc code cleanups and fixes.