Author: plessy Date: 2010-01-25 04:58:06 +0000 (Mon, 25 Jan 2010) New Revision: 4582
Added: trunk/packages/velvet/trunk/debian/README.source trunk/packages/velvet/trunk/debian/patches/ trunk/packages/velvet/trunk/debian/patches/include_debians_zlib.patch trunk/packages/velvet/trunk/debian/upstream-metadata.yaml Removed: trunk/packages/velvet/trunk/debian/reference Modified: trunk/packages/velvet/trunk/debian/changelog trunk/packages/velvet/trunk/debian/copyright trunk/packages/velvet/trunk/debian/rules Log: New upstream release. Zlib convenience copy removed from Debian source package. Added: trunk/packages/velvet/trunk/debian/README.source =================================================================== --- trunk/packages/velvet/trunk/debian/README.source (rev 0) +++ trunk/packages/velvet/trunk/debian/README.source 2010-01-25 04:58:06 UTC (rev 4582) @@ -0,0 +1,21 @@ +Repacked source package. +──────────────────────── + +The original sources were downloaded from +http://www.ebi.ac.uk/~zerbino/velvet/velvet_0.7.56.tgz and repacked after +removing the third-party directory and renaming the main directory +velvet-0.7.56~nozlibcopy, in order to not have to document all copyright +notices in third-party/zlib-1.2.3. + + -- Charles Plessy <[email protected]> Mon, 25 Jan 2010 13:03:06 +0900 + + +This package uses a patch system. +───────────────────────────────── + +A patch, placed in the ‘debian/patches’ directory is applied and unapplied at +build time (but not at unpack time) using the ‘simple-patchsys’ system of CDBS. +The ‘patch’ and ‘unpatch’ targets of debian/rules allow to apply and unapply +the patch. Please refer to the documentation of CDBS for more information. + + -- Charles Plessy <[email protected]> Mon, 25 Jan 2010 13:03:06 +0900 Modified: trunk/packages/velvet/trunk/debian/changelog =================================================================== --- trunk/packages/velvet/trunk/debian/changelog 2010-01-24 16:31:56 UTC (rev 4581) +++ trunk/packages/velvet/trunk/debian/changelog 2010-01-25 04:58:06 UTC (rev 4582) @@ -1,3 +1,18 @@ +velvet (0.7.56~nozlibcopy-1) unstable; urgency=low + + * New upstream version. + * Repackaged the upstream directory to remove the convenience copy + of the zlib. Documented this in ‘debian/README.source’. + Closes: #561433. + * Updated debian/copyright. + * Added ‘include_debians_zlib.patch’ to enforce the use of + /usr/include/zlib.h. This patch is applied using CDBS, see + ‘debian/rules’ and ‘debian/README.source’. + * Renamed ‘debian/reference’ ‘debian/upstream-metadata.yaml’ and + centralised upstream-specific information there. + + -- Charles Plessy <[email protected]> Mon, 25 Jan 2010 13:03:06 +0900 + velvet (0.7.55-1) unstable; urgency=low * New upstream version Modified: trunk/packages/velvet/trunk/debian/copyright =================================================================== --- trunk/packages/velvet/trunk/debian/copyright 2010-01-24 16:31:56 UTC (rev 4581) +++ trunk/packages/velvet/trunk/debian/copyright 2010-01-25 04:58:06 UTC (rev 4582) @@ -2,9 +2,9 @@ Name : Velvet Contact : Daniel Zerbino <[email protected]> -Source : http://www.ebi.ac.uk/~zerbino/velvet/velvet_0.7.53.tgz +Source : http://www.ebi.ac.uk/~zerbino/velvet/velvet_0.7.56.tgz -Copyright: © 2006-2009 Daniel Zerbino <[email protected]> +Copyright: © 2006-2010 Daniel Zerbino <[email protected]> © 2000-2005 Guy St.C. Slater <[email protected]> © 2009 John Marshall <[email protected]> © 2009 David Studholme <[email protected]> @@ -77,38 +77,16 @@ SUCH DAMAGE. Files: contrib/afg_handling/*, contrib/VelvetOptimiser/* -Copyright: © 2008 Simon Gladman <[email protected]> +Copyright: © 2008,2009 Simon Gladman <[email protected]> License: GPL-2+ -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 - appreciated but is not required. - 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: contrib/layout/* Copyright: © 2008 Paul Harrison ([email protected]) License: GPL-2+ Files: contrib/estimate-exp_cov/velvet-estimate-exp_cov.pl, - contrib/observed-insert-length.pl/observed-insert-length.pl + contrib/observed-insert-length.pl/observed-insert-length.pl, + contrib/show_repeats/show_repeats.pl Copyright: 2009, Torsten Seemann 2009, Daniel Zerbino License: GPL-3+ Added: trunk/packages/velvet/trunk/debian/patches/include_debians_zlib.patch =================================================================== --- trunk/packages/velvet/trunk/debian/patches/include_debians_zlib.patch (rev 0) +++ trunk/packages/velvet/trunk/debian/patches/include_debians_zlib.patch 2010-01-25 04:58:06 UTC (rev 4582) @@ -0,0 +1,14 @@ +Description: Use the zlib distributed by Debian, not the one in third-party/zlib-1.2.3/. +Author: Charles Plessy <[email protected]> +Forwarded: no +--- src/readSet.c.orig 2010-01-25 13:27:24.000000000 +0900 ++++ src/readSet.c 2010-01-25 13:28:00.000000000 +0900 +@@ -32,7 +32,7 @@ + #if defined(_WIN32) || defined(__WIN32__) || defined(WIN32) + #include "../third-party/zlib-1.2.3/Win32/include/zlib.h" + #else +-#include "../third-party/zlib-1.2.3/zlib.h" ++#include <zlib.h> + #endif + + #if defined(MSDOS) || defined(OS2) || defined(WIN32) || defined(__CYGWIN__) Deleted: trunk/packages/velvet/trunk/debian/reference =================================================================== --- trunk/packages/velvet/trunk/debian/reference 2010-01-24 16:31:56 UTC (rev 4581) +++ trunk/packages/velvet/trunk/debian/reference 2010-01-25 04:58:06 UTC (rev 4582) @@ -1,12 +0,0 @@ -...@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 2010-01-24 16:31:56 UTC (rev 4581) +++ trunk/packages/velvet/trunk/debian/rules 2010-01-25 04:58:06 UTC (rev 4582) @@ -7,6 +7,7 @@ include /usr/share/cdbs/1/rules/debhelper.mk include /usr/share/cdbs/1/class/makefile.mk +include /usr/share/cdbs/1/rules/simple-patchsys.mk clean:: $(RM) zlib Copied: trunk/packages/velvet/trunk/debian/upstream-metadata.yaml (from rev 4581, trunk/packages/velvet/trunk/debian/reference) =================================================================== --- trunk/packages/velvet/trunk/debian/upstream-metadata.yaml (rev 0) +++ trunk/packages/velvet/trunk/debian/upstream-metadata.yaml 2010-01-25 04:58:06 UTC (rev 4582) @@ -0,0 +1,17 @@ +Contact: Daniel Zerbino <[email protected]> +DOI: 10.1101/gr.074492.107 +Homepage: http://www.ebi.ac.uk/~zerbino/velvet/ +Name: Velvet +PMID: 18349386 +Reference: + 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 + year: 2008 + URL: http://genome.cshlp.org/content/18/5/821.abstract + eprint: http://genome.cshlp.org/content/18/5/821.full.pdf+html +Repository: http://github.com/dzerbino/velvet +Watch: http://www.ebi.ac.uk/~zerbino/velvet/velvet_([.\d]*).tgz _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
