[med-svn] r182 - in trunk/packages: . sibsim4 sibsim4/tags
sibsim4/tags/0.14-1 sibsim4/tags/0.14-1/debian
sibsim4/tags/0.14-1/debian/patches sibsim4/trunk
sibsim4/trunk/debian sibsim4/trunk/debian/patches
Nelson A. de Oliveira
naoliv at alioth.debian.org
Thu Jan 11 19:03:34 CET 2007
Author: naoliv
Date: 2007-01-11 19:03:33 +0100 (Thu, 11 Jan 2007)
New Revision: 182
Added:
trunk/packages/sibsim4/
trunk/packages/sibsim4/branches/
trunk/packages/sibsim4/tags/
trunk/packages/sibsim4/tags/0.14-1/
trunk/packages/sibsim4/tags/0.14-1/debian/
trunk/packages/sibsim4/tags/0.14-1/debian/changelog
trunk/packages/sibsim4/tags/0.14-1/debian/compat
trunk/packages/sibsim4/tags/0.14-1/debian/control
trunk/packages/sibsim4/tags/0.14-1/debian/copyright
trunk/packages/sibsim4/tags/0.14-1/debian/dirs
trunk/packages/sibsim4/tags/0.14-1/debian/install
trunk/packages/sibsim4/tags/0.14-1/debian/manpages
trunk/packages/sibsim4/tags/0.14-1/debian/patches/
trunk/packages/sibsim4/tags/0.14-1/debian/patches/Makefile.patch
trunk/packages/sibsim4/tags/0.14-1/debian/rules
trunk/packages/sibsim4/tags/0.14-1/debian/watch
trunk/packages/sibsim4/trunk/
trunk/packages/sibsim4/trunk/debian/
trunk/packages/sibsim4/trunk/debian/changelog
trunk/packages/sibsim4/trunk/debian/compat
trunk/packages/sibsim4/trunk/debian/control
trunk/packages/sibsim4/trunk/debian/copyright
trunk/packages/sibsim4/trunk/debian/dirs
trunk/packages/sibsim4/trunk/debian/install
trunk/packages/sibsim4/trunk/debian/manpages
trunk/packages/sibsim4/trunk/debian/patches/
trunk/packages/sibsim4/trunk/debian/patches/Makefile.patch
trunk/packages/sibsim4/trunk/debian/rules
trunk/packages/sibsim4/trunk/debian/watch
Log:
New sibsim4 package
Added: trunk/packages/sibsim4/tags/0.14-1/debian/changelog
===================================================================
--- trunk/packages/sibsim4/tags/0.14-1/debian/changelog 2007-01-11 00:58:36 UTC (rev 181)
+++ trunk/packages/sibsim4/tags/0.14-1/debian/changelog 2007-01-11 18:03:33 UTC (rev 182)
@@ -0,0 +1,6 @@
+sibsim4 (0.14-1) unstable; urgency=low
+
+ * Initial release (Closes: #406286).
+
+ -- Nelson A. de Oliveira <naoliv at debian.org> Wed, 10 Jan 2007 02:13:20 -0200
+
Added: trunk/packages/sibsim4/tags/0.14-1/debian/compat
===================================================================
--- trunk/packages/sibsim4/tags/0.14-1/debian/compat 2007-01-11 00:58:36 UTC (rev 181)
+++ trunk/packages/sibsim4/tags/0.14-1/debian/compat 2007-01-11 18:03:33 UTC (rev 182)
@@ -0,0 +1 @@
+5
Added: trunk/packages/sibsim4/tags/0.14-1/debian/control
===================================================================
--- trunk/packages/sibsim4/tags/0.14-1/debian/control 2007-01-11 00:58:36 UTC (rev 181)
+++ trunk/packages/sibsim4/tags/0.14-1/debian/control 2007-01-11 18:03:33 UTC (rev 182)
@@ -0,0 +1,23 @@
+Source: sibsim4
+Section: science
+Priority: optional
+Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Nelson A. de Oliveira <naoliv at debian.org>
+Build-Depends: cdbs, debhelper (>= 5)
+Standards-Version: 3.7.2
+
+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.
+ .
+ Homepage: http://sibsim4.sourceforge.net/
Added: trunk/packages/sibsim4/tags/0.14-1/debian/copyright
===================================================================
--- trunk/packages/sibsim4/tags/0.14-1/debian/copyright 2007-01-11 00:58:36 UTC (rev 181)
+++ trunk/packages/sibsim4/tags/0.14-1/debian/copyright 2007-01-11 18:03:33 UTC (rev 182)
@@ -0,0 +1,44 @@
+This package was debianized by Nelson A. de Oliveira <naoliv at debian.org> on
+Wed, 10 Jan 2007 02:13:20 -0200.
+
+It was downloaded from http://sourceforge.net/projects/sibsim4/
+
+Upstream Authors: Christian Iseli <Christian.Iseli at licr.org>
+ Claudio Lottaz
+
+Copyright: 2001-2006 Swiss Institute of Bioinformatics, and Ludwig Institute
+ for Cancer Research (LICR)
+
+This package implements the Sim4 algorithm for aligning expressed DNA
+with genomic sequences, described in the paper:
+
+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.
+
+Portions copyright by:
+
+Copyright (C) 1998-2001 Liliana Florea
+Copyright (C) 1998-2001 Scott Schwartz
+
+License:
+
+ 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'.
+
+The Debian packaging is (C) 2007, Nelson A. de Oliveira <naoliv at debian.org> and
+is licensed under the GPL, see above.
Added: trunk/packages/sibsim4/tags/0.14-1/debian/dirs
===================================================================
--- trunk/packages/sibsim4/tags/0.14-1/debian/dirs 2007-01-11 00:58:36 UTC (rev 181)
+++ trunk/packages/sibsim4/tags/0.14-1/debian/dirs 2007-01-11 18:03:33 UTC (rev 182)
@@ -0,0 +1,2 @@
+usr/bin
+usr/share/man/man1
Added: trunk/packages/sibsim4/tags/0.14-1/debian/install
===================================================================
--- trunk/packages/sibsim4/tags/0.14-1/debian/install 2007-01-11 00:58:36 UTC (rev 181)
+++ trunk/packages/sibsim4/tags/0.14-1/debian/install 2007-01-11 18:03:33 UTC (rev 182)
@@ -0,0 +1 @@
+SIBsim4 usr/bin
Added: trunk/packages/sibsim4/tags/0.14-1/debian/manpages
===================================================================
--- trunk/packages/sibsim4/tags/0.14-1/debian/manpages 2007-01-11 00:58:36 UTC (rev 181)
+++ trunk/packages/sibsim4/tags/0.14-1/debian/manpages 2007-01-11 18:03:33 UTC (rev 182)
@@ -0,0 +1 @@
+SIBsim4.1
Added: trunk/packages/sibsim4/tags/0.14-1/debian/patches/Makefile.patch
===================================================================
--- trunk/packages/sibsim4/tags/0.14-1/debian/patches/Makefile.patch 2007-01-11 00:58:36 UTC (rev 181)
+++ trunk/packages/sibsim4/tags/0.14-1/debian/patches/Makefile.patch 2007-01-11 18:03:33 UTC (rev 182)
@@ -0,0 +1,21 @@
+diff -Nur sibsim4-0.14/Makefile sibsim4-0.14.new/Makefile
+--- sibsim4-0.14/Makefile 2005-03-22 18:58:01.000000000 -0300
++++ sibsim4-0.14.new/Makefile 2007-01-10 02:28:24.000000000 -0200
+@@ -6,7 +6,7 @@
+ # Copyright (C) 1998-2001 Liliana Florea.
+
+
+-DEBUG =
++DEBUG = -g
+
+
+ # For better performance, replace ``-O'' with whatever
+@@ -14,7 +14,7 @@
+ # For Sun's compilers under Solaris, ``-fast'' works well.
+ # For gcc, ``-O2'' works well.
+
+-OPT = -O
++OPT = -O2
+
+
+ # The default CFLAGS is meant for GCC. If you compile for Solaris, you need
Added: trunk/packages/sibsim4/tags/0.14-1/debian/rules
===================================================================
--- trunk/packages/sibsim4/tags/0.14-1/debian/rules 2007-01-11 00:58:36 UTC (rev 181)
+++ trunk/packages/sibsim4/tags/0.14-1/debian/rules 2007-01-11 18:03:33 UTC (rev 182)
@@ -0,0 +1,5 @@
+#!/usr/bin/make -f
+
+include /usr/share/cdbs/1/rules/simple-patchsys.mk
+include /usr/share/cdbs/1/rules/debhelper.mk
+include /usr/share/cdbs/1/class/makefile.mk
Property changes on: trunk/packages/sibsim4/tags/0.14-1/debian/rules
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/sibsim4/tags/0.14-1/debian/watch
===================================================================
--- trunk/packages/sibsim4/tags/0.14-1/debian/watch 2007-01-11 00:58:36 UTC (rev 181)
+++ trunk/packages/sibsim4/tags/0.14-1/debian/watch 2007-01-11 18:03:33 UTC (rev 182)
@@ -0,0 +1,2 @@
+version=3
+http://sf.net/sibsim4/SIBsim4-(.*)\.tar\.gz
Added: trunk/packages/sibsim4/trunk/debian/changelog
===================================================================
--- trunk/packages/sibsim4/trunk/debian/changelog 2007-01-11 00:58:36 UTC (rev 181)
+++ trunk/packages/sibsim4/trunk/debian/changelog 2007-01-11 18:03:33 UTC (rev 182)
@@ -0,0 +1,6 @@
+sibsim4 (0.14-1) unstable; urgency=low
+
+ * Initial release (Closes: #406286).
+
+ -- Nelson A. de Oliveira <naoliv at debian.org> Wed, 10 Jan 2007 02:13:20 -0200
+
Added: trunk/packages/sibsim4/trunk/debian/compat
===================================================================
--- trunk/packages/sibsim4/trunk/debian/compat 2007-01-11 00:58:36 UTC (rev 181)
+++ trunk/packages/sibsim4/trunk/debian/compat 2007-01-11 18:03:33 UTC (rev 182)
@@ -0,0 +1 @@
+5
Added: trunk/packages/sibsim4/trunk/debian/control
===================================================================
--- trunk/packages/sibsim4/trunk/debian/control 2007-01-11 00:58:36 UTC (rev 181)
+++ trunk/packages/sibsim4/trunk/debian/control 2007-01-11 18:03:33 UTC (rev 182)
@@ -0,0 +1,23 @@
+Source: sibsim4
+Section: science
+Priority: optional
+Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Nelson A. de Oliveira <naoliv at debian.org>
+Build-Depends: cdbs, debhelper (>= 5)
+Standards-Version: 3.7.2
+
+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.
+ .
+ Homepage: http://sibsim4.sourceforge.net/
Added: trunk/packages/sibsim4/trunk/debian/copyright
===================================================================
--- trunk/packages/sibsim4/trunk/debian/copyright 2007-01-11 00:58:36 UTC (rev 181)
+++ trunk/packages/sibsim4/trunk/debian/copyright 2007-01-11 18:03:33 UTC (rev 182)
@@ -0,0 +1,44 @@
+This package was debianized by Nelson A. de Oliveira <naoliv at debian.org> on
+Wed, 10 Jan 2007 02:13:20 -0200.
+
+It was downloaded from http://sourceforge.net/projects/sibsim4/
+
+Upstream Authors: Christian Iseli <Christian.Iseli at licr.org>
+ Claudio Lottaz
+
+Copyright: 2001-2006 Swiss Institute of Bioinformatics, and Ludwig Institute
+ for Cancer Research (LICR)
+
+This package implements the Sim4 algorithm for aligning expressed DNA
+with genomic sequences, described in the paper:
+
+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.
+
+Portions copyright by:
+
+Copyright (C) 1998-2001 Liliana Florea
+Copyright (C) 1998-2001 Scott Schwartz
+
+License:
+
+ 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'.
+
+The Debian packaging is (C) 2007, Nelson A. de Oliveira <naoliv at debian.org> and
+is licensed under the GPL, see above.
Added: trunk/packages/sibsim4/trunk/debian/dirs
===================================================================
--- trunk/packages/sibsim4/trunk/debian/dirs 2007-01-11 00:58:36 UTC (rev 181)
+++ trunk/packages/sibsim4/trunk/debian/dirs 2007-01-11 18:03:33 UTC (rev 182)
@@ -0,0 +1,2 @@
+usr/bin
+usr/share/man/man1
Added: trunk/packages/sibsim4/trunk/debian/install
===================================================================
--- trunk/packages/sibsim4/trunk/debian/install 2007-01-11 00:58:36 UTC (rev 181)
+++ trunk/packages/sibsim4/trunk/debian/install 2007-01-11 18:03:33 UTC (rev 182)
@@ -0,0 +1 @@
+SIBsim4 usr/bin
Added: trunk/packages/sibsim4/trunk/debian/manpages
===================================================================
--- trunk/packages/sibsim4/trunk/debian/manpages 2007-01-11 00:58:36 UTC (rev 181)
+++ trunk/packages/sibsim4/trunk/debian/manpages 2007-01-11 18:03:33 UTC (rev 182)
@@ -0,0 +1 @@
+SIBsim4.1
Added: trunk/packages/sibsim4/trunk/debian/patches/Makefile.patch
===================================================================
--- trunk/packages/sibsim4/trunk/debian/patches/Makefile.patch 2007-01-11 00:58:36 UTC (rev 181)
+++ trunk/packages/sibsim4/trunk/debian/patches/Makefile.patch 2007-01-11 18:03:33 UTC (rev 182)
@@ -0,0 +1,21 @@
+diff -Nur sibsim4-0.14/Makefile sibsim4-0.14.new/Makefile
+--- sibsim4-0.14/Makefile 2005-03-22 18:58:01.000000000 -0300
++++ sibsim4-0.14.new/Makefile 2007-01-10 02:28:24.000000000 -0200
+@@ -6,7 +6,7 @@
+ # Copyright (C) 1998-2001 Liliana Florea.
+
+
+-DEBUG =
++DEBUG = -g
+
+
+ # For better performance, replace ``-O'' with whatever
+@@ -14,7 +14,7 @@
+ # For Sun's compilers under Solaris, ``-fast'' works well.
+ # For gcc, ``-O2'' works well.
+
+-OPT = -O
++OPT = -O2
+
+
+ # The default CFLAGS is meant for GCC. If you compile for Solaris, you need
Added: trunk/packages/sibsim4/trunk/debian/rules
===================================================================
--- trunk/packages/sibsim4/trunk/debian/rules 2007-01-11 00:58:36 UTC (rev 181)
+++ trunk/packages/sibsim4/trunk/debian/rules 2007-01-11 18:03:33 UTC (rev 182)
@@ -0,0 +1,5 @@
+#!/usr/bin/make -f
+
+include /usr/share/cdbs/1/rules/simple-patchsys.mk
+include /usr/share/cdbs/1/rules/debhelper.mk
+include /usr/share/cdbs/1/class/makefile.mk
Property changes on: trunk/packages/sibsim4/trunk/debian/rules
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/sibsim4/trunk/debian/watch
===================================================================
--- trunk/packages/sibsim4/trunk/debian/watch 2007-01-11 00:58:36 UTC (rev 181)
+++ trunk/packages/sibsim4/trunk/debian/watch 2007-01-11 18:03:33 UTC (rev 182)
@@ -0,0 +1,2 @@
+version=3
+http://sf.net/sibsim4/SIBsim4-(.*)\.tar\.gz
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