[med-svn] r10529 - in trunk/packages/soap: . soapsnp soapsnp/debian soapsnp/debian/patches soapsnp/debian/source
Steffen Möller
moeller at alioth.debian.org
Sun Apr 22 23:58:30 UTC 2012
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 <moeller at debian.org> 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 <moeller at debian.org> 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 <moeller at debian.org>
+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 <soap at genomics.org.cn>
+License: GPL-3.0+
+
+Files: debian/*
+Copyright: 2012 Steffen Moeller <moeller at debian.org>
+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
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