Author: moeller Date: 2012-04-21 22:08:43 +0000 (Sat, 21 Apr 2012) New Revision: 10480
Added: trunk/packages/soap/ trunk/packages/soap/README trunk/packages/soap/soap2/ trunk/packages/soap/soap2/debian/ trunk/packages/soap/soap2/debian/README.Debian trunk/packages/soap/soap2/debian/README.source trunk/packages/soap/soap2/debian/changelog trunk/packages/soap/soap2/debian/compat trunk/packages/soap/soap2/debian/control trunk/packages/soap/soap2/debian/copyright trunk/packages/soap/soap2/debian/docs trunk/packages/soap/soap2/debian/patches/ trunk/packages/soap/soap2/debian/patches/compiler_options.patch trunk/packages/soap/soap2/debian/patches/series trunk/packages/soap/soap2/debian/rules trunk/packages/soap/soap2/debian/soap2.install trunk/packages/soap/soap2/debian/soap2.manpages trunk/packages/soap/soap2/debian/source/ trunk/packages/soap/soap2/debian/source/format trunk/packages/soap/soap2/debian/watch.ex Log: Added first shot at a package for the SOAPaligner/soap2 from http://soap.genomics.org.cn . Added: trunk/packages/soap/README =================================================================== --- trunk/packages/soap/README (rev 0) +++ trunk/packages/soap/README 2012-04-21 22:08:43 UTC (rev 10480) @@ -0,0 +1,3 @@ +In this directory we address the packaging of the various +tools surrounding the SOAP sequencing alignment tools from +http://soap.genomics.org.cn. Added: trunk/packages/soap/soap2/debian/README.Debian =================================================================== --- trunk/packages/soap/soap2/debian/README.Debian (rev 0) +++ trunk/packages/soap/soap2/debian/README.Debian 2012-04-21 22:08:43 UTC (rev 10480) @@ -0,0 +1,6 @@ +soap2 for Debian +---------------- + +The authors of this package demand the amd64 platform. + + -- Steffen Moeller <[email protected]> Sat, 21 Apr 2012 22:45:08 +0200 Added: trunk/packages/soap/soap2/debian/README.source =================================================================== --- trunk/packages/soap/soap2/debian/README.source (rev 0) +++ trunk/packages/soap/soap2/debian/README.source 2012-04-21 22:08:43 UTC (rev 10480) @@ -0,0 +1,5 @@ +soap2 for Debian +---------------- + +Only -O2 compilation is performed to keep maximal compatibility across platforms. The patch changes the Makefile accordingly. + Added: trunk/packages/soap/soap2/debian/changelog =================================================================== --- trunk/packages/soap/soap2/debian/changelog (rev 0) +++ trunk/packages/soap/soap2/debian/changelog 2012-04-21 22:08:43 UTC (rev 10480) @@ -0,0 +1,5 @@ +soap2 (2.20-1) UNRELEASED; urgency=low + + * Initial release (Closes: #669917) + + -- Steffen Moeller <[email protected]> Sat, 21 Apr 2012 22:45:08 +0200 Added: trunk/packages/soap/soap2/debian/compat =================================================================== --- trunk/packages/soap/soap2/debian/compat (rev 0) +++ trunk/packages/soap/soap2/debian/compat 2012-04-21 22:08:43 UTC (rev 10480) @@ -0,0 +1 @@ +8 Added: trunk/packages/soap/soap2/debian/control =================================================================== --- trunk/packages/soap/soap2/debian/control (rev 0) +++ trunk/packages/soap/soap2/debian/control 2012-04-21 22:08:43 UTC (rev 10480) @@ -0,0 +1,34 @@ +Source: soap2 +Section: science +Priority: optional +Maintainer: Steffen Moeller <[email protected]> +Build-Depends: debhelper (>= 8.0.0) +Standards-Version: 3.9.3 +Vcs-Browser: http://svn.debian.org/viewvc/debian-med/trunk/packages/bioperl/trunk/ +Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/bioperl/trunk/ +Homepage: http://soap.genomics.org.cn/soapaligner.html + +Package: soap2 +Architecture: any +Depends: ${shlibs:Depends}, ${misc:Depends} +Description: aligner of short reads of next generation sequencers + This package addresses a common problem in bioinformatics that has + become routine now also in clinical research: the assembly and + comparison of the very long genomic DNA sequences from many + short reads that the machines provide. + . + SOAPaligner/soap2 is a member of the Short Oligonucleotide Analysis + Package (SOAP) and an updated version of SOAP software for short + oligonucleotide alignment (soap v1). The new program features in super + fast and accurate alignment for huge amounts of short reads generated by + Illumina/Solexa Genome Analyzer. Compared to soap v1, it is one order + of magnitude faster. It require only 2 minutes aligning one million + single-end reads onto the human reference genome. Another remarkable + improvement of SOAPaligner is that it now supports a wide range of the + read length. + . + SOAPaligner/soap2 benefitted in time and space efficiency by a revolution + in the basic data structures and algorithms used. The core algorithms and + the indexing data structures (2way-BWT) are developed by the algorithms + research group of the Department of Computer Science, the University + of Hong Kong (T.W. Lam, Alan Tam, Simon Wong, Edward Wu and S.M. Yiu). Added: trunk/packages/soap/soap2/debian/copyright =================================================================== --- trunk/packages/soap/soap2/debian/copyright (rev 0) +++ trunk/packages/soap/soap2/debian/copyright 2012-04-21 22:08:43 UTC (rev 10480) @@ -0,0 +1,56 @@ +Format: http://dep.debian.net/deps/dep5 +Upstream-Name: soap2 +Source: http://soap.genomics.org.cn/soapaligner.html + +Files: * +Copyright: 2004 Wong Chi Kwong + 2009 BGI Shenzhen, Chang Yu <[email protected]> +License: GPL-3.0+ + +Files: stdaln.c +Copyright: 2003-2006, 2008 Heng Li <[email protected]> +License: MIT + +Files: debian/* +Copyright: 2012 Steffen Moeller <[email protected]> +License: GPL-3.0+ + +License: GPL-3.0+ + 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 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 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". + + +License: MIT + Permission is hereby granted, free of charge, to any person obtaining + a copy of this software and associated documentation files (the + "Software"), to deal in the Software without restriction, including + without limitation the rights to use, copy, modify, merge, publish, + distribute, sublicense, and/or sell copies of the Software, and to + permit persons to whom the Software is furnished to do so, subject to + the following conditions: + . + The above copyright notice and this permission notice shall be + included in all copies or substantial portions of the Software. + . + THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF + MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS + BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN + ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN + CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE + SOFTWARE. + Added: trunk/packages/soap/soap2/debian/docs =================================================================== --- trunk/packages/soap/soap2/debian/docs (rev 0) +++ trunk/packages/soap/soap2/debian/docs 2012-04-21 22:08:43 UTC (rev 10480) @@ -0,0 +1 @@ +NEWS Added: trunk/packages/soap/soap2/debian/patches/compiler_options.patch =================================================================== --- trunk/packages/soap/soap2/debian/patches/compiler_options.patch (rev 0) +++ trunk/packages/soap/soap2/debian/patches/compiler_options.patch 2012-04-21 22:08:43 UTC (rev 10480) @@ -0,0 +1,22 @@ +Index: soap2-2.20/Makefile +=================================================================== +--- soap2-2.20.orig/Makefile 2009-07-23 00:49:31.000000000 +0200 ++++ soap2-2.20/Makefile 2012-04-22 00:01:01.446041368 +0200 +@@ -6,7 +6,7 @@ + CC = gcc + DEBUG_FLAGS = -g3 -Wall -O2 + PROFILE_FLAGS = -fprofile-arcs -ftest-coverage -pg +-RELEASE_FLAGS = -msse3 -O3 -static -funroll-loops -maccumulate-outgoing-args -fomit-frame-pointer ++RELEASE_FLAGS = $(DEBUG_FLAGS) + STATIC_FLAGS = -static + DFLAGS = -DMAKE_TIME=\""`date`"\" + LIBS = -lm +@@ -18,7 +18,7 @@ + DFLAGS += -DDEBUG + # PTHREADS = NO + else +- CFLAGS = $(RELEASE_FLAGS) $(STATIC_FLAGS) ++ CFLAGS = $(RELEASE_FLAGS) + endif + + ifeq (YES, $(PTHREADS)) Added: trunk/packages/soap/soap2/debian/patches/series =================================================================== --- trunk/packages/soap/soap2/debian/patches/series (rev 0) +++ trunk/packages/soap/soap2/debian/patches/series 2012-04-21 22:08:43 UTC (rev 10480) @@ -0,0 +1 @@ +compiler_options.patch Added: trunk/packages/soap/soap2/debian/rules =================================================================== --- trunk/packages/soap/soap2/debian/rules (rev 0) +++ trunk/packages/soap/soap2/debian/rules 2012-04-21 22:08:43 UTC (rev 10480) @@ -0,0 +1,8 @@ +#!/usr/bin/make -f +# -*- makefile -*- + +# Uncomment this to turn on verbose mode. +#export DH_VERBOSE=1 + +%: + dh $@ Property changes on: trunk/packages/soap/soap2/debian/rules ___________________________________________________________________ Added: svn:executable + * Added: trunk/packages/soap/soap2/debian/soap2.install =================================================================== --- trunk/packages/soap/soap2/debian/soap2.install (rev 0) +++ trunk/packages/soap/soap2/debian/soap2.install 2012-04-21 22:08:43 UTC (rev 10480) @@ -0,0 +1 @@ +soap usr/bin Added: trunk/packages/soap/soap2/debian/soap2.manpages =================================================================== --- trunk/packages/soap/soap2/debian/soap2.manpages (rev 0) +++ trunk/packages/soap/soap2/debian/soap2.manpages 2012-04-21 22:08:43 UTC (rev 10480) @@ -0,0 +1 @@ +soap.1 Added: trunk/packages/soap/soap2/debian/source/format =================================================================== --- trunk/packages/soap/soap2/debian/source/format (rev 0) +++ trunk/packages/soap/soap2/debian/source/format 2012-04-21 22:08:43 UTC (rev 10480) @@ -0,0 +1 @@ +3.0 (quilt) Added: trunk/packages/soap/soap2/debian/watch.ex =================================================================== --- trunk/packages/soap/soap2/debian/watch.ex (rev 0) +++ trunk/packages/soap/soap2/debian/watch.ex 2012-04-21 22:08:43 UTC (rev 10480) @@ -0,0 +1,23 @@ +# Example watch control file for uscan +# Rename this file to "watch" and then you can run the "uscan" command +# to check for upstream updates and more. +# See uscan(1) for format + +# Compulsory line, this is a version 3 file +version=3 + +# Uncomment to examine a Webpage +# <Webpage URL> <string match> +#http://www.example.com/downloads.php soap2-(.*)\.tar\.gz + +# Uncomment to examine a Webserver directory +#http://www.example.com/pub/soap2-(.*)\.tar\.gz + +# Uncommment to examine a FTP server +#ftp://ftp.example.com/pub/soap2-(.*)\.tar\.gz debian uupdate + +# Uncomment to find new files on sourceforge, for devscripts >= 2.9 +# http://sf.net/soap2/soap2-(.*)\.tar\.gz + +# Uncomment to find new files on GooglePages +# http://example.googlepages.com/foo.html soap2-(.*)\.tar\.gz _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
