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commit ef9b9d27e82b26d1851f66cb3af42c64601bdc75 Author: Andreas Tille <[email protected]> Date: Fri Feb 7 17:04:06 2014 +0100 Add initial debian/ dir --- debian/changelog | 5 +++++ debian/compat | 1 + debian/control | 37 +++++++++++++++++++++++++++++++++++++ debian/copyright | 36 ++++++++++++++++++++++++++++++++++++ debian/docs | 1 + debian/get-orig-source | 27 +++++++++++++++++++++++++++ debian/install | 1 + debian/links | 2 ++ debian/rules | 13 +++++++++++++ debian/source/format | 1 + debian/upstream | 12 ++++++++++++ debian/watch | 5 +++++ 12 files changed, 141 insertions(+) diff --git a/debian/changelog b/debian/changelog new file mode 100644 index 0000000..67b3a6e --- /dev/null +++ b/debian/changelog @@ -0,0 +1,5 @@ +fitgpc (0.0.20130418-1) UNRELEASED; urgency=low + + * Initial release (Closes: #<bug>) + + -- Andreas Tille <[email protected]> Fri, 07 Feb 2014 11:38:38 +0100 diff --git a/debian/compat b/debian/compat new file mode 100644 index 0000000..ec63514 --- /dev/null +++ b/debian/compat @@ -0,0 +1 @@ +9 diff --git a/debian/control b/debian/control new file mode 100644 index 0000000..762a670 --- /dev/null +++ b/debian/control @@ -0,0 +1,37 @@ +Source: fitgpc +Maintainer: Debian Med Packaging Team <[email protected]> +Uploaders: Andreas Tille <[email protected]> +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. + diff --git a/debian/copyright b/debian/copyright new file mode 100644 index 0000000..d2b2bbb --- /dev/null +++ b/debian/copyright @@ -0,0 +1,36 @@ +Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Upstream-Name: fitGCP +Upstream-Contact: Martin S. Lindner <[email protected]> +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 <[email protected]> +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. + diff --git a/debian/docs b/debian/docs new file mode 100644 index 0000000..ab1a32b --- /dev/null +++ b/debian/docs @@ -0,0 +1 @@ +README* diff --git a/debian/get-orig-source b/debian/get-orig-source new file mode 100755 index 0000000..5f52f51 --- /dev/null +++ b/debian/get-orig-source @@ -0,0 +1,27 @@ +#!/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} diff --git a/debian/install b/debian/install new file mode 100644 index 0000000..1469e75 --- /dev/null +++ b/debian/install @@ -0,0 +1 @@ +fitGCP.py usr/share/fitgcp diff --git a/debian/links b/debian/links new file mode 100644 index 0000000..adba8ed --- /dev/null +++ b/debian/links @@ -0,0 +1,2 @@ +usr/share/fitgcp/fitGCP.py usr/bin/fitgcp + diff --git a/debian/rules b/debian/rules new file mode 100755 index 0000000..ca47e3b --- /dev/null +++ b/debian/rules @@ -0,0 +1,13 @@ +#!/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 diff --git a/debian/source/format b/debian/source/format new file mode 100644 index 0000000..163aaf8 --- /dev/null +++ b/debian/source/format @@ -0,0 +1 @@ +3.0 (quilt) diff --git a/debian/upstream b/debian/upstream new file mode 100644 index 0000000..8b5596d --- /dev/null +++ b/debian/upstream @@ -0,0 +1,12 @@ +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 diff --git a/debian/watch b/debian/watch new file mode 100644 index 0000000..69ec119 --- /dev/null +++ b/debian/watch @@ -0,0 +1,5 @@ +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) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/fitgpc.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
