[med-svn] r3476 - trunk/packages/velvet/trunk/debian
Charles Plessy
plessy at alioth.debian.org
Wed Jun 10 02:44:18 UTC 2009
Author: plessy
Date: 2009-06-10 02:44:18 +0000 (Wed, 10 Jun 2009)
New Revision: 3476
Modified:
trunk/packages/velvet/trunk/debian/changelog
trunk/packages/velvet/trunk/debian/copyright
trunk/packages/velvet/trunk/debian/install
trunk/packages/velvet/trunk/debian/rules
Log:
New upstream release; minor trouble to autogenerate the manpages.
* New upstream release correcting multiple bugs, changing the stats output,
allowing optional scaffolding and multiple rounds of Pebble.
* Added the programs velveth_de and velvetg_de to the package in /usr/bin,
and the scripts shuffleSequences_fasta.pl and shuffleSequences_fastq.pl in
/usr/share/velvet (debian/rules, debian/install).
* Refreshed debian/copyright.
* Temporarly disabled the manpage generation of velvetg* because the --help
option is not available (debian/rules).
Modified: trunk/packages/velvet/trunk/debian/changelog
===================================================================
--- trunk/packages/velvet/trunk/debian/changelog 2009-06-09 23:25:37 UTC (rev 3475)
+++ trunk/packages/velvet/trunk/debian/changelog 2009-06-10 02:44:18 UTC (rev 3476)
@@ -1,3 +1,16 @@
+velvet (0.7.34-1) unstable; urgency=low
+
+ * New upstream release correcting multiple bugs, changing the stats output,
+ allowing optional scaffolding and multiple rounds of Pebble.
+ * Added the programs velveth_de and velvetg_de to the package in /usr/bin,
+ and the scripts shuffleSequences_fasta.pl and shuffleSequences_fastq.pl in
+ /usr/share/velvet (debian/rules, debian/install).
+ * Refreshed debian/copyright.
+ * Temporarly disabled the manpage generation of velvetg* because the --help
+ option is not available (debian/rules).
+
+ -- Charles Plessy <plessy at debian.org> Tue, 09 Jun 2009 21:28:03 +0900
+
velvet (0.7.31-1) unstable; urgency=low
* New upstream version
Modified: trunk/packages/velvet/trunk/debian/copyright
===================================================================
--- trunk/packages/velvet/trunk/debian/copyright 2009-06-09 23:25:37 UTC (rev 3475)
+++ trunk/packages/velvet/trunk/debian/copyright 2009-06-10 02:44:18 UTC (rev 3476)
@@ -1,30 +1,79 @@
-Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat
-Upstream-Name: Velvet
-Upstream-Maintainer: Daniel Zerbino,
- John-Mark Gurney (Fibonacci heap implementation),
- Guy Slater (memory management routines),
- Ewan Birney (hashing function)
-Upstream-Source: http://www.ebi.ac.uk/~zerbino/velvet/velvet_0.7.24.tgz
+Format: Machine-readable license summary, see ‘http://dep.debian.net/deps/dep5/’.
+Name: Velvet
+Contact: Daniel Zerbino <zerbino at ebi.ac.uk>
+Source: http://www.ebi.ac.uk/~zerbino/velvet/velvet_0.7.34.tgz
-Files: *
-Copyright: © 2006-2008 Daniel Zerbino
+Copyright: © 2006-2009 Daniel Zerbino <zerbino at ebi.ac.uk>
+ © 2000-2005 Guy St.C. Slater <guy at ebi.ac.uk>
+ © 2009 John Marshall (jm18 at sanger.ac.uk)
License: GPL-2+
- This program is free software; you can redistribute it and/or modify
+ This file is part of Velvet.
+ .
+ Velvet 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 program is distributed in the hope that it will be useful,
+ Velvet 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 program; if not, write to the Free Software Foundation, Inc.,
- 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
-X-Comment: On Debian systems, the complete text of the GNU General Public
- License can be found in `/usr/share/common-licenses/GPL'.
+ You should have received a copy of the GNU General Public License
+ along with Velvet; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+Comment: On Debian systems, the complete text of the GNU General Public
+ License version 2 can be found in ‘/usr/share/common-licenses/GPL-2’.
+Files: velvet_0.7.34/src/fibpriv.h
+ velvet_0.7.34/src/dfib.c
+ velvet_0.7.34/src/fib.h
+ velvet_0.7.34/src/fib.c
+ velvet_0.7.34/src/dfib.h
+ velvet_0.7.34/src/dfibpriv.h
+License: GPL-2+ and other.
+ Copyright 2007, 2008 Daniel Zerbino (zerbino at ebi.ac.uk)
+ .
+ This file is part of Velvet.
+ .
+ Velvet 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.
+ .
+ Velvet 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 Velvet; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+ .
+ Copyright 1997, 1999-2003 John-Mark Gurney.
+ All rights reserved.
+ .
+ Redistribution and use in source and binary forms, with or without
+ .
+ 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.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE AUTHOR 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 AUTHOR 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: /third-party/afg_handling/*
Copyright: © 2008 Simon Gladman <simon.gladman at csiro.au>
License: GPL-2+
@@ -57,5 +106,5 @@
Files: debian/*
Copyright: 2008-2009 Charles Plessy <plessy at debian.org>
- 2008 Andreas Tille <tille at debian.org>,
+ 2008-2009 Andreas Tille <tille at debian.org>,
License: Same as velvet
Modified: trunk/packages/velvet/trunk/debian/install
===================================================================
--- trunk/packages/velvet/trunk/debian/install 2009-06-09 23:25:37 UTC (rev 3475)
+++ trunk/packages/velvet/trunk/debian/install 2009-06-10 02:44:18 UTC (rev 3476)
@@ -1,2 +1,2 @@
-velvetg usr/bin
-velveth usr/bin
+velvet* usr/bin
+shuffl* usr/share/velvet
Modified: trunk/packages/velvet/trunk/debian/rules
===================================================================
--- trunk/packages/velvet/trunk/debian/rules 2009-06-09 23:25:37 UTC (rev 3475)
+++ trunk/packages/velvet/trunk/debian/rules 2009-06-10 02:44:18 UTC (rev 3476)
@@ -11,9 +11,15 @@
DEB_MAKE_BUILD_TARGET = obj velveth velvetg Z_LIB_FILES='' LDFLAGS='-lm -lz' OPT='' Z_LIB_INC='/usr/include'
build/velvet::
+ make color Z_LIB_FILES='' LDFLAGS='-lm -lz' OPT='' Z_LIB_INC='/usr/include'
mkdir -p $(CURDIR)/debian/$(pkg)/usr/share/man/man1/
help2man --no-info --name="simple hashing program" \
$(CURDIR)/velveth > $(CURDIR)/debian/$(pkg)/usr/share/man/man1/velveth.1
- help2man --no-info --version-option=" " \
- --name="de Bruijn graph construction, error removal and repeat resolution" \
- $(CURDIR)/velvetg > $(CURDIR)/debian/$(pkg)/usr/share/man/man1/velvetg.1
+ help2man --no-info --name="simple hashing program (colorspace version)" \
+ $(CURDIR)/velveth_de > $(CURDIR)/debian/$(pkg)/usr/share/man/man1/velveth_de.1
+# help2man --no-info --version-option=" " \
+# --name="de Bruijn graph construction, error removal and repeat resolution" \
+# $(CURDIR)/velvetg > $(CURDIR)/debian/$(pkg)/usr/share/man/man1/velvetg.1
+# help2man --no-info --version-option=" " \
+# --name="de Bruijn graph construction, error removal and repeat resolution (colorspace version)" \
+# $(CURDIR)/velvetg_de > $(CURDIR)/debian/$(pkg)/usr/share/man/man1/velvetg_de.1
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