Author: moeller Date: 2012-04-22 23:58:30 +0000 (Sun, 22 Apr 2012) New Revision: 10529
Added: trunk/packages/soap/soapsnp/ trunk/packages/soap/soapsnp/debian/ trunk/packages/soap/soapsnp/debian/README.Debian trunk/packages/soap/soapsnp/debian/README.source trunk/packages/soap/soapsnp/debian/changelog trunk/packages/soap/soapsnp/debian/compat trunk/packages/soap/soapsnp/debian/control trunk/packages/soap/soapsnp/debian/copyright trunk/packages/soap/soapsnp/debian/docs trunk/packages/soap/soapsnp/debian/patches/ trunk/packages/soap/soapsnp/debian/patches/Makefile.patch trunk/packages/soap/soapsnp/debian/patches/series trunk/packages/soap/soapsnp/debian/rules trunk/packages/soap/soapsnp/debian/source/ trunk/packages/soap/soapsnp/debian/source/format trunk/packages/soap/soapsnp/debian/watch.ex Log: A second tool for the SOAP collection of tools for NGsequence data analysis. Added: trunk/packages/soap/soapsnp/debian/README.Debian =================================================================== --- trunk/packages/soap/soapsnp/debian/README.Debian (rev 0) +++ trunk/packages/soap/soapsnp/debian/README.Debian 2012-04-22 23:58:30 UTC (rev 10529) @@ -0,0 +1,11 @@ +soapsnp for Debian +------------------ + +** PACKAGING IS NOT YET COMPLETED ** + +Ideas for improvements of this package: + * platform-specific optimisations + * debian/watch should be crafted + * we should have some public use cases together with getData + + -- Steffen Moeller <[email protected]> Sun, 22 Apr 2012 01:26:41 +0200 Added: trunk/packages/soap/soapsnp/debian/README.source =================================================================== --- trunk/packages/soap/soapsnp/debian/README.source (rev 0) +++ trunk/packages/soap/soapsnp/debian/README.source 2012-04-22 23:58:30 UTC (rev 10529) @@ -0,0 +1,5 @@ +soapsnp for Debian +------------------ + +The man page was built with help2man and manually edited. + Added: trunk/packages/soap/soapsnp/debian/changelog =================================================================== --- trunk/packages/soap/soapsnp/debian/changelog (rev 0) +++ trunk/packages/soap/soapsnp/debian/changelog 2012-04-22 23:58:30 UTC (rev 10529) @@ -0,0 +1,5 @@ +soapsnp (1.03-1) unstable; urgency=low + + * Initial release (Closes: #nnnn) + + -- Steffen Moeller <[email protected]> Sun, 22 Apr 2012 01:26:41 +0200 Added: trunk/packages/soap/soapsnp/debian/compat =================================================================== --- trunk/packages/soap/soapsnp/debian/compat (rev 0) +++ trunk/packages/soap/soapsnp/debian/compat 2012-04-22 23:58:30 UTC (rev 10529) @@ -0,0 +1 @@ +8 Added: trunk/packages/soap/soapsnp/debian/control =================================================================== --- trunk/packages/soap/soapsnp/debian/control (rev 0) +++ trunk/packages/soap/soapsnp/debian/control 2012-04-22 23:58:30 UTC (rev 10529) @@ -0,0 +1,34 @@ +Source: soapsnp +Section: science +Priority: optional +Maintainer: Steffen Moeller <[email protected]> +Build-Depends: debhelper (>= 8.0.0), libboost-iostreams-dev +Standards-Version: 3.9.3 +Vcs-Browser: http://svn.debian.org/viewvc/debian-med/trunk/packages/soapsnp/ +Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/soapsnp/ +Homepage: http://soap.genomics.org.cn/soapsnp.html + +Package: soapsnp +Architecture: any +Depends: ${shlibs:Depends}, ${misc:Depends} +Suggests: genomics.cn-soapsnp +Description: <insert up to 60 chars description> + For getting ideas on the cause of diseases or their response to + therapy, and for understanding either for a particular patient, + doctors around the globe are starting to look at the genes or the + whole genome and how that sequence is different from a healthy / + well responding individual. + . + SOAPsnp is a member of the SOAP (Short Oligonucleotide Analysis + Package). The program is a resequencing utility. It assembles the + consensus sequence for the genome of a newly sequenced individual based + on the alignment of the raw sequencing reads on a known reference. SNPs + can then be identified on the consensus sequence through the comparison + with the reference. + . + SOAPsnp uses a method based on Bayes' theorem (the reverse probability + model) to call consensus genotype by carefully considering the data + quality, alignment, and recurring experimental errors. All these kinds + of information was integrated into a single quality score for each base + in PHRED scale to measure the accuracy of consensus calling. Currently, + it supports the alignment format of SOAPaligner (soap2). Added: trunk/packages/soap/soapsnp/debian/copyright =================================================================== --- trunk/packages/soap/soapsnp/debian/copyright (rev 0) +++ trunk/packages/soap/soapsnp/debian/copyright 2012-04-22 23:58:30 UTC (rev 10529) @@ -0,0 +1,28 @@ +Format: http://dep.debian.net/deps/dep5 +Upstream-Name: soapsnp +Source: <url://example.com> + +Files: * +Copyright: 2008 BGI shenzhen <[email protected]> +License: GPL-3.0+ + +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". Added: trunk/packages/soap/soapsnp/debian/docs =================================================================== --- trunk/packages/soap/soapsnp/debian/docs (rev 0) +++ trunk/packages/soap/soapsnp/debian/docs 2012-04-22 23:58:30 UTC (rev 10529) @@ -0,0 +1 @@ +readme Added: trunk/packages/soap/soapsnp/debian/patches/Makefile.patch =================================================================== --- trunk/packages/soap/soapsnp/debian/patches/Makefile.patch (rev 0) +++ trunk/packages/soap/soapsnp/debian/patches/Makefile.patch 2012-04-22 23:58:30 UTC (rev 10529) @@ -0,0 +1,12 @@ +Index: soapsnp-1.03/makefile +=================================================================== +--- soapsnp-1.03.orig/makefile 2009-05-25 09:49:19.000000000 +0200 ++++ soapsnp-1.03/makefile 2012-04-22 01:27:43.714978426 +0200 +@@ -1,6 +1,6 @@ + DEFINE = + CXX = g++ +-CXXFLAGS = -fomit-frame-pointer -O3 -ffast-math -funroll-loops -mmmx -msse -msse2 -msse3 -fmessage-length=0 #-MMD -MP -MF #-g3 -Wall -maccumulate-outgoing-args ++CXXFLAGS = -fomit-frame-pointer -O3 -ffast-math -funroll-loops #-mmmx -msse -msse2 -msse3 -fmessage-length=0 #-MMD -MP -MF #-g3 -Wall -maccumulate-outgoing-args + + LFLAGS = -lz + Added: trunk/packages/soap/soapsnp/debian/patches/series =================================================================== --- trunk/packages/soap/soapsnp/debian/patches/series (rev 0) +++ trunk/packages/soap/soapsnp/debian/patches/series 2012-04-22 23:58:30 UTC (rev 10529) @@ -0,0 +1 @@ +Makefile.patch Added: trunk/packages/soap/soapsnp/debian/rules =================================================================== --- trunk/packages/soap/soapsnp/debian/rules (rev 0) +++ trunk/packages/soap/soapsnp/debian/rules 2012-04-22 23:58:30 UTC (rev 10529) @@ -0,0 +1,13 @@ +#!/usr/bin/make -f +# -*- makefile -*- +# Sample debian/rules that uses debhelper. +# This file was originally written by Joey Hess and Craig Small. +# As a special exception, when this file is copied by dh-make into a +# dh-make output file, you may use that output file without restriction. +# This special exception was added by Craig Small in version 0.37 of dh-make. + +# Uncomment this to turn on verbose mode. +#export DH_VERBOSE=1 + +%: + dh $@ Property changes on: trunk/packages/soap/soapsnp/debian/rules ___________________________________________________________________ Added: svn:executable + * Added: trunk/packages/soap/soapsnp/debian/source/format =================================================================== --- trunk/packages/soap/soapsnp/debian/source/format (rev 0) +++ trunk/packages/soap/soapsnp/debian/source/format 2012-04-22 23:58:30 UTC (rev 10529) @@ -0,0 +1 @@ +3.0 (quilt) Added: trunk/packages/soap/soapsnp/debian/watch.ex =================================================================== --- trunk/packages/soap/soapsnp/debian/watch.ex (rev 0) +++ trunk/packages/soap/soapsnp/debian/watch.ex 2012-04-22 23:58:30 UTC (rev 10529) @@ -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 soapsnp-(.*)\.tar\.gz + +# Uncomment to examine a Webserver directory +#http://www.example.com/pub/soapsnp-(.*)\.tar\.gz + +# Uncommment to examine a FTP server +#ftp://ftp.example.com/pub/soapsnp-(.*)\.tar\.gz debian uupdate + +# Uncomment to find new files on sourceforge, for devscripts >= 2.9 +# http://sf.net/soapsnp/soapsnp-(.*)\.tar\.gz + +# Uncomment to find new files on GooglePages +# http://example.googlepages.com/foo.html soapsnp-(.*)\.tar\.gz _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
