Commit ef9b9d27 authored by Andreas Tille's avatar Andreas Tille

Add initial debian/ dir

parent 915099fd
fitgpc (0.0.20130418-1) UNRELEASED; urgency=low
* Initial release (Closes: #<bug>)
-- Andreas Tille <tille@debian.org> Fri, 07 Feb 2014 11:38:38 +0100
Source: fitgpc
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>
Section: science
Priority: optional
Build-Depends: debhelper (>= 9),
python-all-dev
Standards-Version: 3.9.5
Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/fitgpc.git
Vcs-Git: git://anonscm.debian.org/debian-med/fitgpc.git
Homepage: http://sourceforge.net/projects/fitgcp/
X-Python-Version: >= 2.6
Package: fitgpc
Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends},
${python:Depends},
python-scipy,
python-numpy
Description: fitting genome coverage distributions with mixture models
Genome coverage, the number of sequencing reads mapped to a position in
a genome, is an insightful indicator of irregularities within sequencing
experiments. While the average genome coverage is frequently used within
algorithms in computational genomics, the complete information available
in coverage profiles (i.e. histograms over all coverages) is currently
not exploited to its full extent. Thus, biases such as fragmented or
erroneous reference genomes often remain unaccounted for. Making this
information accessible can improve the quality of sequencing experiments
and quantitative analyses.
.
fitGCP is a framework for fitting mixtures of probability distributions
to genome coverage profiles. Besides commonly used distributions, fitGCP
uses distributions tailored to account for common artifacts. The mixture
models are iteratively fitted based on the Expectation-Maximization
algorithm.
Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: fitGCP
Upstream-Contact: Martin S. Lindner <LindnerM@rki.de>
Source: http://sourceforge.net/projects/fitgcp/files/
Files: *
Copyright: 2012-2013 Martin S. Lindner and Maximilian Kollock
Robert Koch-Institut
License: BSDlike
Files: debian/*
Copyright: 2014 Andreas Tille <tille@debian.org>
License: BSDlike
License: BSDlike
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright
notice, this list of conditions and the following disclaimer in the
documentation and/or other materials provided with the distribution.
* The name of the author may not be used to endorse or promote products
derived from this software without specific prior written permission.
.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL MARTIN S. LINDNER BE LIABLE FOR ANY
DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#!/bin/sh
# get source for mrbayes to obtain documentation source from SVN
set -e
# set -x
NAME=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'`
COMPRESSION=xz
VERSION=`dpkg-parsechangelog | awk '/^Version:/ { print $2 }' | sed 's/\([0-9\.]\+\)-[0-9]\+$/\1/'`
mkdir -p ../tarballs
cd ../tarballs
TARDIR=${NAME}-${VERSION}
# fetch source from SVN
svn export svn://svn.code.sf.net/p/fitgcp/code/trunk $TARDIR
cd $TARDIR
recode ibmpc.. fitGCP.py
mv fitGCP.py fitGCP.py.bak
echo '#!/usr/bin/python' > fitGCP.py
cat fitGCP.py.bak >> fitGCP.py
touch -r fitGCP.py.bak fitGCP.py
rm fitGCP.py.bak
wget http://sourceforge.net/projects/fitgcp/files/README.txt
cd ..
GZIP="--best --no-name" XZ_OPT="-6v" tar --owner=root --group=root --mode=a+rX -a -cf ${NAME}_${VERSION}.orig.tar.${COMPRESSION} ${TARDIR}
rm -rf ${TARDIR}
fitGCP.py usr/share/fitgcp
usr/share/fitgcp/fitGCP.py usr/bin/fitgcp
#!/usr/bin/make -f
# DH_VERBOSE := 1
%:
dh $@ --with python2
override_dh_fixperms:
dh_fixperms
find debian -name "*.py" -exec chmod 755 \{\} \;
get-orig-source:
. debian/get-orig-source
Reference:
Author: Martin S. Lindner and Maximilian Kollock and Franziska Zickmann and Bernhard Y. Renard
Title: Analyzing genome coverage profiles with applications to quality control in metagenomics
Journal: Bioinformatics
Year: 2013
Volume: 29
Number: 10
Pages: 1260-1267
DOI: 10.1093/bioinformatics/btt147
PMID: 23589648
URL: http://bioinformatics.oxfordjournals.org/content/29/10/1260
eprint: http://bioinformatics.oxfordjournals.org/content/29/10/1260.full.pdf+html
version=3
# unfortunately watch files does not work since upstream has no version numbers
# see http://sourceforge.net/projects/arden/files/ARDEN/
#
# http://sf.net/fitgcp/fitGCP-VM-([0-9.]+)\.(?:tgz|tar\.gz|tar\.xz|tar\.bz2|zip)
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