[med-svn] r10480 - in trunk/packages: . soap soap/soap2 soap/soap2/debian soap/soap2/debian/patches soap/soap2/debian/source
Steffen Möller
moeller at alioth.debian.org
Sat Apr 21 22:08:43 UTC 2012
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 <moeller at debian.org> 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 <moeller at debian.org> 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 <moeller at debian.org>
+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 <yuchang at genomics.org.cn>
+License: GPL-3.0+
+
+Files: stdaln.c
+Copyright: 2003-2006, 2008 Heng Li <lh3lh3 at gmail.com>
+License: MIT
+
+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".
+
+
+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
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