debian/0000755000000000000000000000000011702000766007165 5ustar debian/upstream-metadata.yaml0000644000000000000000000000066211525340776013506 0ustar Contact: Xavier Didelot 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 debian/manpages0000644000000000000000000000001311525332372010701 0ustar debian/*.1 debian/source/0000755000000000000000000000000011520762120010462 5ustar debian/source/format0000644000000000000000000000001411473514012011672 0ustar 3.0 (quilt) debian/install0000644000000000000000000000003111525335646010563 0ustar bin/ClonalFrame usr/bin debian/copyright0000644000000000000000000000236411667613727011146 0ustar Format: http://dep.debian.net/deps/dep5/ Upstream-Name: ClonalFrame Upstream-Contact: Xavier Didelot Source: http://www.xavierdidelot.xtreemhost.com/clonalframe.htm Files: * Copyright: © 2009-2010 Xavier Didelot License: GPL-2+ ClonalFrame 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 2 of the License, or (at your option) any later version. . ClonalFrame 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 Velvet; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA Comment: On Debian systems, the complete text of the GNU General Public License version 2 can be found in ‘/usr/share/common-licenses/GPL-2’. Files: debian/* Copyright: © 2011 Andreas Tille License: PD The packaging work is in the public domain unless stated otherwise. debian/rules0000755000000000000000000000046411702000736010246 0ustar #!/usr/bin/make -f # debian/rules for clonalframe # Andreas Tille # 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 debian/get-orig-source0000644000000000000000000000131211521301700012107 0ustar #!/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}" debian/patches/0000755000000000000000000000000011603145336010617 5ustar debian/patches/01_gcc-4.6.patch0000644000000000000000000000163611603145336013207 0ustar Author: Sebastian Ramacher Description: Fix gcc-4.6 build issue Closes: #625120 Date: Date: Thu, 30 Jun 2011 18:34:10 +0200 --- clonalframe-1.2.orig/src/move_hidden.cpp +++ clonalframe-1.2/src/move_hidden.cpp @@ -166,7 +166,8 @@ sum+=gsl_matrix_get(f,j,i)*q[j][state][site-siteprev-1]; gsl_matrix_set(f,state,i+1,sum*gsl_matrix_get(e,state,msgs[site])); } - Util::normalize(&(gsl_matrix_column(f,i+1).vector)); + gsl_vector_view view = gsl_matrix_column(f,i+1); + Util::normalize(&view.vector); } return f; } @@ -420,7 +421,8 @@ gsl_matrix_set(e,i+1,2,(1.0-m2)*m3+(1.0-m3)*m2); } - Util::normalize(&(gsl_matrix_row(e,i+1).vector)); + gsl_vector_view view = gsl_matrix_row(e,i+1); + Util::normalize(&view.vector); } } debian/patches/series0000644000000000000000000000002111603144767012034 0ustar 01_gcc-4.6.patch debian/watch0000644000000000000000000000022011531013027010202 0ustar version=3 http://www.xavierdidelot.xtreemhost.com/clonalframe.htm \ http://www.stats.ox.ac.uk/~didelot/files/ClonalFrame-([\d\.]+)\.tar\.gz debian/changelog0000644000000000000000000000137111702000766011041 0ustar clonalframe (1.2-3) unstable; urgency=low [ A. Costa ] * Corrected typos in debian/ClonalFrame.1 (Closes: #650474). [ Andreas Tille ] * debian/control: - Fixed Vcs fields - Remove quilt from build-depends -- Andreas Tille Sat, 07 Jan 2012 09:26:15 +0100 clonalframe (1.2-2) unstable; urgency=low * Fix gcc-4.6 build issue (thanks to Sebastian Ramacher for the patch) Closes: #625120 * Standards-Version: 3.9.2 (no changes needed) * Debhelper 8 (control+compat) -- Andreas Tille Thu, 30 Jun 2011 21:09:59 +0200 clonalframe (1.2-1) unstable; urgency=low * Initial release (Closes: #614657) -- Andreas Tille Fri, 11 Feb 2011 22:52:24 +0100 debian/compat0000644000000000000000000000000211603145155010365 0ustar 8 debian/ClonalFrame.10000644000000000000000000000510011667613727011447 0ustar .TH ClonalFrame "1" "1.2" "February 2011" .SH NAME ClonalFrame \- inference of bacterial microevolution using multilocus sequence data .SH SYNOPSIS ClonalFrame [OPTIONS] inputfile outputfile .SH DESCRIPTION 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. 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 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 uniformly chosen coalescent tree and 2 for UPGMA tree (default) .TP \fB\-w\fR FILE Use Newick file for initial tree .TP \fB\-a\fR NUM Sets the first parameter of the beta prior distribution of nu .TP \fB\-b\fR NUM Sets the second parameter of the beta prior distribution of nu .TP \fB\-U\fR Use uniform priors for rho, theta and delta .TP \fB\-B\fR Run in BURST mode .TP \fB\-C\fR Run in UPGMA mode with a site\-by\-site bootstrap procedure .TP \fB\-c\fR Run in UPGMA mode with a fragment\-by\-fragment bootstrap procedure .TP \fB\-S\fR NUM Sets the seed for the random number generator to NUM .TP \fB\-E\fR NUM Sets the rate of exponential growth (default is 0) .TP \fB\-I\fR Ignores first block in the alignment .TP \fB\-L\fR Clean\-up the alignment before running ClonalFrame .TP \fB\-l\fR Minimum distance between two reference sites (default is 50) .TP \fB\-v\fR Verbose mode .SH AUTHOR \fBClonalFrame\fP was written by Xavier Didelot. .PP This manual page was written by Andreas Tille , for the Debian project (but may be used by others). debian/control0000644000000000000000000000266711702000745010600 0ustar Source: clonalframe Section: science Priority: optional Maintainer: Debian Med Packaging Team DM-Upload-Allowed: yes Uploaders: Andreas Tille Build-Depends: debhelper (>= 8), qt4-qmake, libgsl0-dev, libqt4-dev Standards-Version: 3.9.2 Homepage: http://www.xavierdidelot.xtreemhost.com/clonalframe.htm Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/clonalframe/trunk Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/clonalframe/trunk/ 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.