[med-svn] r5955 - in trunk/packages: . clonalframe clonalframe/trunk clonalframe/trunk/debian clonalframe/trunk/debian/source
Andreas Tille
tille at alioth.debian.org
Fri Feb 11 23:16:36 UTC 2011
Author: tille
Date: 2011-02-11 23:16:34 +0000 (Fri, 11 Feb 2011)
New Revision: 5955
Added:
trunk/packages/clonalframe/
trunk/packages/clonalframe/trunk/
trunk/packages/clonalframe/trunk/debian/
trunk/packages/clonalframe/trunk/debian/ClonalFrame.1
trunk/packages/clonalframe/trunk/debian/changelog
trunk/packages/clonalframe/trunk/debian/compat
trunk/packages/clonalframe/trunk/debian/control
trunk/packages/clonalframe/trunk/debian/copyright
trunk/packages/clonalframe/trunk/debian/get-orig-source
trunk/packages/clonalframe/trunk/debian/install
trunk/packages/clonalframe/trunk/debian/manpages
trunk/packages/clonalframe/trunk/debian/rules
trunk/packages/clonalframe/trunk/debian/source/
trunk/packages/clonalframe/trunk/debian/source/format
trunk/packages/clonalframe/trunk/debian/upstream-metadata.yaml
trunk/packages/clonalframe/trunk/debian/watch
Log:
Inject first shot at clonalframe packaging
Added: trunk/packages/clonalframe/trunk/debian/ClonalFrame.1
===================================================================
--- trunk/packages/clonalframe/trunk/debian/ClonalFrame.1 (rev 0)
+++ trunk/packages/clonalframe/trunk/debian/ClonalFrame.1 2011-02-11 23:16:34 UTC (rev 5955)
@@ -0,0 +1,89 @@
+.TH ClonalFrame "1" "February 2011" "This is ClonalFrame version 1.2" "User Commands"
+.SH NAME
+ClonalFrame \- manual page for This is ClonalFrame version 1.2
+.SH USAGE
+ClonalFrame [OPTIONS] inputfile outputfile
+.SH DESCRIPTION
+This is ClonalFrame version 1.2
+.IP
+Options:
+.TP
+\fB\-x\fR NUM
+Sets the number of iterations after burn\-in (default is 50000)
+.TP
+\fB\-y\fR NUM
+Sets the number of burn\-in iterations (default is 50000)
+.TP
+\fB\-z\fR NUM
+Sets the number of iterations between samples (default is 100)
+.TP
+\fB\-e\fR NUM
+Sets the number of branch\-swapping moves per iterations (default
+.IP
+is so that half of the time is spent branch\-swapping)
+.TP
+\fB\-m\fR NUM
+Sets the initial value of theta to NUM (default is Watterson estimate)
+.TP
+\fB\-d\fR NUM
+Sets the initial value of delta to NUM (default is 0.001)
+.TP
+\fB\-n\fR NUM
+Sets the initial value of nu to NUM (default is 0.01)
+.TP
+\fB\-r\fR NUM
+Sets the initial value of R to NUM (default is initial theta/10)
+.TP
+\fB\-M\fR
+Do update the value of theta
+.TP
+\fB\-D\fR
+Do not update the value of delta
+.TP
+\fB\-N\fR
+Do not update the value of nu
+.TP
+\fB\-R\fR
+Do not update the value of R
+.TP
+\fB\-T\fR
+Do not update the topology
+.TP
+\fB\-A\fR
+Do not update the ages of the nodes
+.TP
+\fB\-G\fR
+Remove all gaps
+.TP
+\fB\-H\fR
+Remove all gaps at non\-polymorphic positions
+.TP
+\fB\-t\fR NUM
+Indicate which initial tree to use: 0 for a null tree, 1 for a
+.IP
+uniformly chosen coalescent tree and 2 for UPGMA tree (default)
+\fB\-w\fR FILE Use Newick file for initial tree
+\fB\-a\fR NUM Sets the first parameter of the beta prior distribution of nu
+\fB\-b\fR NUM Sets the second parameter of the beta prior distribution of nu
+\fB\-U\fR Use uniform priors for rho, theta and delta
+\fB\-B\fR Run in BURST mode
+\fB\-C\fR Run in UPGMA mode with a site\-by\-site boostrap procedure
+\fB\-c\fR Run in UPGMA mode with a fragment\-by\-fragment boostrap procedure
+\fB\-S\fR NUM Sets the seed for the random number generator to NUM
+\fB\-E\fR NUM Sets the rate of exponential growth (default is 0)
+\fB\-I\fR Ignores first block in the alignment
+\fB\-L\fR Clean\-up the alignment before running ClonalFrame
+\fB\-l\fR Minimum distance between two reference sites (default is 50)
+\fB\-v\fR Verbose mode
+.SH "SEE ALSO"
+The full documentation for
+.B This
+is maintained as a Texinfo manual. If the
+.B info
+and
+.B This
+programs are properly installed at your site, the command
+.IP
+.B info This
+.PP
+should give you access to the complete manual.
Added: trunk/packages/clonalframe/trunk/debian/changelog
===================================================================
--- trunk/packages/clonalframe/trunk/debian/changelog (rev 0)
+++ trunk/packages/clonalframe/trunk/debian/changelog 2011-02-11 23:16:34 UTC (rev 5955)
@@ -0,0 +1,5 @@
+clonalframe (1.2-1) unstable; urgency=low
+
+ * Initial release (Closes: #??????)
+
+ -- Andreas Tille <tille at debian.org> Fri, 11 Feb 2011 22:52:24 +0100
Added: trunk/packages/clonalframe/trunk/debian/compat
===================================================================
--- trunk/packages/clonalframe/trunk/debian/compat (rev 0)
+++ trunk/packages/clonalframe/trunk/debian/compat 2011-02-11 23:16:34 UTC (rev 5955)
@@ -0,0 +1 @@
+7
Added: trunk/packages/clonalframe/trunk/debian/control
===================================================================
--- trunk/packages/clonalframe/trunk/debian/control (rev 0)
+++ trunk/packages/clonalframe/trunk/debian/control 2011-02-11 23:16:34 UTC (rev 5955)
@@ -0,0 +1,28 @@
+Source: clonalframe
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Andreas Tille <tille at debian.org>
+Build-Depends: debhelper (>= 7.1), qt4-qmake, libgsl0-dev, libqt4-dev
+Standards-Version: 3.9.1
+Homepage: http://www.xavierdidelot.xtreemhost.com/clonalframe.htm
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/clonalframe/trunk
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/clonalframe/trunk/?rev=0&sc=0
+
+Package: clonalframe
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: inference of bacterial microevolution using multilocus sequence data
+ ClonalFrame identifies the clonal relationships between the members of
+ a sample, while also estimating the chromosomal position of homologous
+ recombination events that have disrupted the clonal inheritance.
+ .
+ ClonalFrame can be applied to any kind of sequence data, from a single
+ fragment of DNA to whole genomes. It is well suited for the analysis of
+ MLST data, where 7 gene fragments have been sequenced, but becomes
+ progressively more powerful as the sequenced regions increase in length
+ and number up to whole genomes. However, it requires the sequences to be
+ aligned. If you have genomic data that is not aligned, we recommend
+ using Mauve which produces alignment of whole bacterial genomes in
+ exactly the format required for analysis with ClonalFrame.
Added: trunk/packages/clonalframe/trunk/debian/copyright
===================================================================
--- trunk/packages/clonalframe/trunk/debian/copyright (rev 0)
+++ trunk/packages/clonalframe/trunk/debian/copyright 2011-02-11 23:16:34 UTC (rev 5955)
@@ -0,0 +1,63 @@
+Format: http://dep.debian.net/deps/dep5/
+Upstream-Name: Bowtie
+Upstream-Contact: Ben Langmead <blangmea at jhsph.edu>
+Source: http://sourceforge.net/projects/bowtie-bio/files/bowtie/
+
+Files: *
+Copyright: © 2009-2010 Ben Langmead, C. Trapnell, M. Pop, Steven L. Salzberg
+License:
+ This program is free software; you can redistribute it and/or modify it
+ under the terms of the "Artistic License" which comes with Debian.
+
+ THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
+ WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES
+ OF MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+
+ On Debian systems, the complete text of the Artistic License
+ can be found in "/usr/share/common-licenses/Artistic".
+
+Files: SeqAn-1.1
+Upstream Authors:
+ Andreas Döring <doering at inf.fu-berlin.de>
+ David Weese <weese at inf.fu-berlin.de>
+ Tobias Rausch <rausch at inf.fu-berlin.de>
+ Stephan Aiche <aiche at inf.fu-berlin.de>
+ Anne-Katrin Emde <emde at inf.fu-berlin.de>
+ Carsten Kemena <kemena at inf.fu-berlin.de>
+ Konrad Ludwig Moritz Rudolph <krudolph at inf.fu-berlin.de>
+ Marcel H. Schulz. <marcel.schulz at molgen.mpg.de>
+Copyright:
+ If not otherwise stated Copyright (C) 2007-2009 the Seqan authors.
+License:
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library 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
+ Lesser General Public License for more details.
+
+ On Debian systems, you can find the LGPL license in:
+ /usr/share/common-licenses/LGPL
+
+File: SeqAn-1.1/seqan/index/index_sa_lss.h
+Copyright:
+ Copyright 1999 N. Jesper Larsson <jesper at cs.lth.se>
+ Copyright 2007 David Weese.
+License:
+ This software may be used freely for any purpose. However, when
+ distributed, the original source must be clearly stated, and, when
+ the source code is distributed, the copyright notice must be retained
+ and any alterations in the code must be clearly marked. No warranty
+ is given regarding the quality of this software.
+
+
+Files: debian/*
+Copyright: © 2010 Files: *
+Copyright: © 2011 Steffen Moeller <moeller at debian.org>,
+ Yask Gupta <yask.gupta87 at gmail.com>
+ © 2011 Andreas Tille <tille at debian.org>
+License: PD
+ The packaging work is in the public domain unless stated otherwise.
Added: trunk/packages/clonalframe/trunk/debian/get-orig-source
===================================================================
--- trunk/packages/clonalframe/trunk/debian/get-orig-source (rev 0)
+++ trunk/packages/clonalframe/trunk/debian/get-orig-source 2011-02-11 23:16:34 UTC (rev 5955)
@@ -0,0 +1,22 @@
+#!/bin/sh
+# script to download and repack source package of bowtie which comes in zip format
+
+PKG=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'`
+VERSION=`uscan --verbose --force-download | \
+ grep "Newest version on remote site is .* local version is .*" | \
+ head -n 1 | \
+ sed "s/Newest version on remote site is \([-0-9.]\+\),.*/\1/"`
+
+mkdir -p ../tarballs
+cd ../tarballs
+
+UPSTREAMDIR=${PKG}-${VERSION}
+unzip ../"${UPSTREAMDIR}-src.zip"
+
+## remove copy of SeqAn library - unfortunately the package does not compile
+## with the Debian packaged version 1.2
+#rm -rf "${UPSTREAMDIR}"/SeqAn-1.1
+
+GZIP="--best --no-name" tar -czf "$PKG"_"$VERSION".orig.tar.gz "${UPSTREAMDIR}"
+rm -rf "${UPSTREAMDIR}"
+
Added: trunk/packages/clonalframe/trunk/debian/install
===================================================================
--- trunk/packages/clonalframe/trunk/debian/install (rev 0)
+++ trunk/packages/clonalframe/trunk/debian/install 2011-02-11 23:16:34 UTC (rev 5955)
@@ -0,0 +1 @@
+bin/ClonalFrame usr/bin
Added: trunk/packages/clonalframe/trunk/debian/manpages
===================================================================
--- trunk/packages/clonalframe/trunk/debian/manpages (rev 0)
+++ trunk/packages/clonalframe/trunk/debian/manpages 2011-02-11 23:16:34 UTC (rev 5955)
@@ -0,0 +1 @@
+debian/*.1
Added: trunk/packages/clonalframe/trunk/debian/rules
===================================================================
--- trunk/packages/clonalframe/trunk/debian/rules (rev 0)
+++ trunk/packages/clonalframe/trunk/debian/rules 2011-02-11 23:16:34 UTC (rev 5955)
@@ -0,0 +1,20 @@
+#!/usr/bin/make -f
+# debian/rules for clonalframe
+# Andreas Tille <tille at debian.org>
+# GPL
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+%:
+ dh $@
+
+override_dh_clean:
+ dh_clean
+ rm -rf bin build Makefile
+
+override_dh_auto_build:
+ qmake; $(MAKE)
+
+get-orig-source:
+ . debian/get-orig-source
Property changes on: trunk/packages/clonalframe/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/clonalframe/trunk/debian/source/format
===================================================================
--- trunk/packages/clonalframe/trunk/debian/source/format (rev 0)
+++ trunk/packages/clonalframe/trunk/debian/source/format 2011-02-11 23:16:34 UTC (rev 5955)
@@ -0,0 +1 @@
+3.0 (quilt)
Added: trunk/packages/clonalframe/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/clonalframe/trunk/debian/upstream-metadata.yaml (rev 0)
+++ trunk/packages/clonalframe/trunk/debian/upstream-metadata.yaml 2011-02-11 23:16:34 UTC (rev 5955)
@@ -0,0 +1,12 @@
+Contact: Xavier Didelot <xavier.didelot at gmail.com>
+DOI: 10.1534/genetics.106.063305
+Homepage: http://www.xavierdidelot.xtreemhost.com/clonalframe.htm
+Name: ClonalFrame
+Reference:
+ author: Xavier Didelot, Daniel Falush
+ title: Inference of Bacterial Microevolution Using Multilocus Sequence Data
+ journal: Genetics Advance
+ volume: 175
+ pages: 1251-1266
+ year: 2006
+ URL: http://www.genetics.org/cgi/content/abstract/175/3/1251
Added: trunk/packages/clonalframe/trunk/debian/watch
===================================================================
--- trunk/packages/clonalframe/trunk/debian/watch (rev 0)
+++ trunk/packages/clonalframe/trunk/debian/watch 2011-02-11 23:16:34 UTC (rev 5955)
@@ -0,0 +1,2 @@
+version=3
+http://sf.net/bowtie-bio/bowtie-([\d\.]+)-src\.zip
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