Author: plessy
Date: 2009-07-11 15:34:53 +0000 (Sat, 11 Jul 2009)
New Revision: 3614
Added:
trunk/packages/velvet/trunk/debian/reference
Removed:
trunk/packages/velvet/trunk/debian/README.source
trunk/packages/velvet/trunk/debian/examples
trunk/packages/velvet/trunk/debian/patches/
Modified:
trunk/packages/velvet/trunk/debian/README.Debian
trunk/packages/velvet/trunk/debian/changelog
trunk/packages/velvet/trunk/debian/control
trunk/packages/velvet/trunk/debian/copyright
trunk/packages/velvet/trunk/debian/install
trunk/packages/velvet/trunk/debian/rules
Log:
New upstream release and packaging polishing.
* New upstream release.
* Added bibliographic information in BibTeX format in debian/references.
* debian/rules: touch zlib to avoid third-party zlib to be built.
* Removed
?\226?\128?\152debian/patches/20_external_zlib.patch?\226?\128?\153. Passing
apropriate
variables in debian/rules is enough to build dynamically on Debian's
zlib.
* Removed the quilt patch system (debian/control, debian/README.source
debian/rules).
* Incremented Standards-Version in debian/control to reflect conformance
with Policy 3.8.2 (no changes needed).
* Corrected the installation of files that were moved from the
?\226?\128?\152third-party?\226?\128?\153 directory to the
?\226?\128?\152contrib?\226?\128?\153 directory.
* Experimentation on debian/copyright.
Modified: trunk/packages/velvet/trunk/debian/README.Debian
===================================================================
--- trunk/packages/velvet/trunk/debian/README.Debian 2009-07-11 06:53:09 UTC
(rev 3613)
+++ trunk/packages/velvet/trunk/debian/README.Debian 2009-07-11 15:34:53 UTC
(rev 3614)
@@ -1,6 +1,6 @@
-velvet for Debian
+Velvet for Debian
-----------------
-Third party scripts have been placed in /usr/share/velvet.
+Third party scripts have been placed in ‘/usr/share/velvet/contrib’.
- -- Charles Plessy <[email protected]> Tue, 13 Jan 2009 00:06:25 +0900
+ -- Charles Plessy <[email protected]> Sat, 11 Jul 2009 18:06:40 +0900
Deleted: trunk/packages/velvet/trunk/debian/README.source
===================================================================
--- trunk/packages/velvet/trunk/debian/README.source 2009-07-11 06:53:09 UTC
(rev 3613)
+++ trunk/packages/velvet/trunk/debian/README.source 2009-07-11 15:34:53 UTC
(rev 3614)
@@ -1,2 +0,0 @@
-This packages uses a patch system. Please read
-/usr/share/doc/quilt/README.source for more informations.
Modified: trunk/packages/velvet/trunk/debian/changelog
===================================================================
--- trunk/packages/velvet/trunk/debian/changelog 2009-07-11 06:53:09 UTC
(rev 3613)
+++ trunk/packages/velvet/trunk/debian/changelog 2009-07-11 15:34:53 UTC
(rev 3614)
@@ -1,3 +1,21 @@
+velvet (0.7.44-1) unstable; urgency=low
+
+ * New upstream release.
+ * Added bibliographic information in BibTeX format in debian/references.
+ * debian/rules: touch zlib to avoid third-party zlib to be built.
+ * Removed ‘debian/patches/20_external_zlib.patch’. Passing apropriate
+ variables in debian/rules is enough to build dynamically on Debian's
+ zlib.
+ * Removed the quilt patch system (debian/control, debian/README.source
+ debian/rules).
+ * Incremented Standards-Version in debian/control to reflect conformance
+ with Policy 3.8.2 (no changes needed).
+ * Corrected the installation of files that were moved from the
+ ‘third-party’ directory to the ‘contrib’ directory.
+ * Experimentation on debian/copyright.
+
+ -- Charles Plessy <[email protected]> Sun, 12 Jul 2009 00:24:56 +0900
+
velvet (0.7.37-1) unstable; urgency=low
* New upstream release.
Modified: trunk/packages/velvet/trunk/debian/control
===================================================================
--- trunk/packages/velvet/trunk/debian/control 2009-07-11 06:53:09 UTC (rev
3613)
+++ trunk/packages/velvet/trunk/debian/control 2009-07-11 15:34:53 UTC (rev
3614)
@@ -5,8 +5,8 @@
DM-Upload-Allowed: yes
Uploaders: Charles Plessy <[email protected]>,
Andreas Tille <[email protected]>
-Build-Depends: cdbs, debhelper (>= 7), zlib1g-dev, quilt, help2man
-Standards-Version: 3.8.1
+Build-Depends: cdbs, debhelper (>= 7), zlib1g-dev, help2man
+Standards-Version: 3.8.2
Homepage: http://www.ebi.ac.uk/~zerbino/velvet/
Vcs-Browser:
http://svn.debian.org/wsvn/debian-med/trunk/packages/velvet/trunk/?rev=0&sc=0
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/velvet/trunk/
@@ -24,10 +24,6 @@
Velvet currently takes in short read sequences, removes errors then produces
high quality unique contigs. It then uses paired read information, if
available, to retrieve the repeated areas between contigs.
- .
- Velvet was published in: `Velvet: algorithms for de novo short read assembly
- using de Bruijn graphs. D.R. Zerbino and E. Birney. Genome Research
- 18:821-829.'
Package: velvet-example
Architecture: all
Modified: trunk/packages/velvet/trunk/debian/copyright
===================================================================
--- trunk/packages/velvet/trunk/debian/copyright 2009-07-11 06:53:09 UTC
(rev 3613)
+++ trunk/packages/velvet/trunk/debian/copyright 2009-07-11 15:34:53 UTC
(rev 3614)
@@ -1,67 +1,68 @@
Machine-readable license summary, see ‘http://dep.debian.net/deps/dep5/’.
-Name: Velvet
-Contact: Daniel Zerbino <[email protected]>
-Source: http://www.ebi.ac.uk/~zerbino/velvet/velvet_0.7.37.tgz
+Name : Velvet
+Contact : Daniel Zerbino <[email protected]>
+Source : http://www.ebi.ac.uk/~zerbino/velvet/velvet_0.7.44.tgz
Copyright: © 2006-2009 Daniel Zerbino <[email protected]>
© 2000-2005 Guy St.C. Slater <[email protected]>
© 2009 John Marshall ([email protected])
License: GPL-2+
- 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
+
+ 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
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
+Files: src/fibpriv.h
+ src/dfib.c
+ src/fib.h
+ src/fib.c
+ src/dfib.h
+ src/dfibpriv.h
License: GPL-2+ and other.
Copyright 2007, 2008 Daniel Zerbino ([email protected])
- .
+
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
@@ -74,22 +75,22 @@
OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
SUCH DAMAGE.
-Files: /third-party/afg_handling/*
+Files: contrib/afg_handling/*, contrib/VelvetOptimiser/*
Copyright: © 2008 Simon Gladman <[email protected]>
License: GPL-2+
-Files: /third-party/z-lib-1.2.3
+Files: third-party/z-lib-1.2.3
Name: zlib
Copyright: © 1995-1998 Jean-loup Gailly and Mark Adler
License:
This software is provided 'as-is', without any express or implied
warranty. In no event will the authors be held liable for any damages
arising from the use of this software.
- .
+
Permission is granted to anyone to use this software for any purpose,
including commercial applications, and to alter it and redistribute it
freely, subject to the following restrictions:
- .
+
1. The origin of this software must not be misrepresented; you must not
claim that you wrote the original software. If you use this software
in a product, an acknowledgment in the product documentation would be
@@ -97,14 +98,33 @@
2. Altered source versions must be plainly marked as such, and must not be
misrepresented as being the original software.
3. This notice may not be removed or altered from any source distribution.
- .
+
Jean-loup Gailly Mark Adler
[email protected] [email protected]
-Files: third-party/layout/*
+Files: contrib/layout/*
Copyright: © 2008 Paul Harrison ([email protected])
License: GPL-2+
+Files: contrib/estimate-exp_cov/velvet-estimate-exp_cov.pl
+Copyright: 2009, Torsten Seemann
+License: GPL-3+
+ This program 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 3 of the License, or
+ (at your option) any later version.
+
+ This program 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, see <http://www.gnu.org/licenses/>.
+
+On Debian systems, the complete text of the GNU General Public
+License version 3 can be found in ‘/usr/share/common-licenses/GPL-3’.
+
Files: debian/*
Copyright: 2008-2009 Charles Plessy <[email protected]>
2008-2009 Andreas Tille <[email protected]>,
Deleted: trunk/packages/velvet/trunk/debian/examples
===================================================================
--- trunk/packages/velvet/trunk/debian/examples 2009-07-11 06:53:09 UTC (rev
3613)
+++ trunk/packages/velvet/trunk/debian/examples 2009-07-11 15:34:53 UTC (rev
3614)
@@ -1,2 +0,0 @@
-third-party/layout
-third-party/afg_handling
Modified: trunk/packages/velvet/trunk/debian/install
===================================================================
--- trunk/packages/velvet/trunk/debian/install 2009-07-11 06:53:09 UTC (rev
3613)
+++ trunk/packages/velvet/trunk/debian/install 2009-07-11 15:34:53 UTC (rev
3614)
@@ -1,2 +1,3 @@
velvet* usr/bin
shuffl* usr/share/velvet
+contrib usr/share/velvet/contrib
Added: trunk/packages/velvet/trunk/debian/reference
===================================================================
--- trunk/packages/velvet/trunk/debian/reference
(rev 0)
+++ trunk/packages/velvet/trunk/debian/reference 2009-07-11 15:34:53 UTC
(rev 3614)
@@ -0,0 +1,12 @@
+...@article{daniel R.Zerbino052008,
+author = {Zerbino, Daniel R. and Birney, Ewan},
+title={{Velvet: Algorithms for de novo short read assembly using de Bruijn
graphs}},
+journal = {Genome Research},
+volume = {18},
+number = {5},
+pages = {821-829},
+doi = {10.1101/gr.074492.107},
+year = {2008},
+URL = {http://genome.cshlp.org/content/18/5/821.abstract},
+eprint = {http://genome.cshlp.org/content/18/5/821.full.pdf+html}
+}
Modified: trunk/packages/velvet/trunk/debian/rules
===================================================================
--- trunk/packages/velvet/trunk/debian/rules 2009-07-11 06:53:09 UTC (rev
3613)
+++ trunk/packages/velvet/trunk/debian/rules 2009-07-11 15:34:53 UTC (rev
3614)
@@ -2,16 +2,21 @@
DEB_COMPRESS_EXCLUDE := .pdf # The PDF doc will not be compressed
-include /usr/share/cdbs/1/rules/patchsys-quilt.mk
+build/velvet::
+ touch zlib # prevents the zlib in the ‘third-party’ folder to be built.
+
include /usr/share/cdbs/1/rules/debhelper.mk
include /usr/share/cdbs/1/class/makefile.mk
+clean::
+ $(RM) zlib
+
pkg=velvet
-DEB_MAKE_BUILD_TARGET = obj velveth velvetg Z_LIB_FILES='' LDFLAGS='-lm -lz'
OPT='' Z_LIB_INC='/usr/include'
+DEB_MAKE_BUILD_TARGET = obj velveth velvetg Z_LIB_FILES='' LDFLAGS='-lm -lz'
OPT=''
build/velvet::
- make color CFLAGS='$(CFLAGS)' Z_LIB_FILES='' LDFLAGS='-lm -lz' OPT=''
Z_LIB_INC='/usr/include'
+ make color CFLAGS='$(CFLAGS)' Z_LIB_FILES='' LDFLAGS='-lm -lz' OPT=''
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
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