This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository gasic.
commit ffe61b739db53508f9838bbb905014f189d14d57 Author: Andreas Tille <[email protected]> Date: Sat Feb 8 09:22:50 2014 +0100 Add some initial debian/ dir --- debian/changelog | 8 ++++++++ debian/compat | 1 + debian/control | 34 ++++++++++++++++++++++++++++++++++ debian/copyright | 36 ++++++++++++++++++++++++++++++++++++ debian/docs | 2 ++ debian/examples | 1 + debian/get-orig-source | 19 +++++++++++++++++++ debian/install | 2 ++ debian/links | 4 ++++ debian/rules | 9 +++++++++ debian/source/format | 1 + debian/upstream | 12 ++++++++++++ debian/watch | 3 +++ 13 files changed, 132 insertions(+) diff --git a/debian/changelog b/debian/changelog new file mode 100644 index 0000000..d3ebd14 --- /dev/null +++ b/debian/changelog @@ -0,0 +1,8 @@ +gasic (0.0.r18-1) UNRELEASED; urgency=low + + * Initial release (Closes: #<bug>) + TODO: since there is a name conflict with mason and the Debian package + mason is something else than the seqan tool, the code needs to be patched + to find /usr/lib/seqan/bin/mason + + -- Andreas Tille <[email protected]> Sat, 08 Feb 2014 08:47:28 +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..2ca7ba9 --- /dev/null +++ b/debian/control @@ -0,0 +1,34 @@ +Source: gasic +Section: science +Priority: optional +Maintainer: Debian Med Packaging Team <[email protected]> +Uploaders: Andreas Tille <[email protected]> +Build-Depends: debhelper (>= 9), + python-all-dev +Standards-Version: 3.9.5 +Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/gasic.git +Vcs-Git: git://anonscm.debian.org/debian-med/gasic.git +Homepage: http://sourceforge.net/projects/gasic/ + +Package: gasic +Architecture: any +Depends: ${misc:Depends}, + ${python:Depends}, + python-scipy, + python-numpy, + python-biopython, + bowtie, + bowtie2, + bwa, + seqan-apps +Description: Genome Abundance Similarity Correction + One goal of sequencing based metagenomic analysis is the quantitative + taxonomic assessment of microbial community compositions. However, the + majority of approaches either quantify at low resolution (e.g. at phylum + level) or have severe problems discerning highly similar species. Yet, + accurate quantification on species level is desirable in applications + such as metagenomic diagnostics or community comparison. GASiC is a + method to correct read alignment results for the ambiguities imposed by + similarities of genomes. It has superior performance over existing + methods. + diff --git a/debian/copyright b/debian/copyright new file mode 100644 index 0000000..90eaeba --- /dev/null +++ b/debian/copyright @@ -0,0 +1,36 @@ +Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Upstream-Name: GASiC +Upstream-Contact: Martin S. Lindner <[email protected]> +Source: http://sourceforge.net/projects/gasic/files/ + +Files: * +Copyright: 2ß12-2013 Martin S. Lindner <[email protected]> + 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..58eb773 --- /dev/null +++ b/debian/docs @@ -0,0 +1,2 @@ +doc/MANUAL +README diff --git a/debian/examples b/debian/examples new file mode 100644 index 0000000..565e7b4 --- /dev/null +++ b/debian/examples @@ -0,0 +1 @@ +doc/example_script.py diff --git a/debian/get-orig-source b/debian/get-orig-source new file mode 100755 index 0000000..c9c1392 --- /dev/null +++ b/debian/get-orig-source @@ -0,0 +1,19 @@ +#!/bin/sh +# NOTE: The upstream tarball is not up to date - so we drag the source from SVN for the moment +# get source for gasic 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/gasic/code/trunk $TARDIR + +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..1d5bb5f --- /dev/null +++ b/debian/install @@ -0,0 +1,2 @@ +*.py usr/share/gasic +core usr/share/gasic diff --git a/debian/links b/debian/links new file mode 100644 index 0000000..ecfccd3 --- /dev/null +++ b/debian/links @@ -0,0 +1,4 @@ +usr/share/gasic/correct_abundances.py usr/bin/correct_abundances +usr/share/gasic/create_matrix.py usr/bin/create_matrix +usr/share/gasic/quality_check.py usr/bin/quality_check +usr/share/gasic/run_mappers.py usr/bin/run_mappers diff --git a/debian/rules b/debian/rules new file mode 100755 index 0000000..de37bdd --- /dev/null +++ b/debian/rules @@ -0,0 +1,9 @@ +#!/usr/bin/make -f + +# DH_VERBOSE := 1 + +%: + dh $@ --with python2 + +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..6a6265b --- /dev/null +++ b/debian/upstream @@ -0,0 +1,12 @@ +Reference: + Author: Martin S. Lindner and Bernhard Y. Renard + Title: Metagenomic abundance estimation and diagnostic testing on species level + Journal: Nucleic Acids Research + Year: 2013 + Volume: 41 + Number: 1 + Pages: e10 + DOI: 10.1093/nar/gks803 + PMID: 22941661 + URL: http://nar.oxfordjournals.org/content/41/1/e10 + eprint: http://nar.oxfordjournals.org/content/41/1/e10.full.pdf+html diff --git a/debian/watch b/debian/watch new file mode 100644 index 0000000..de12ab0 --- /dev/null +++ b/debian/watch @@ -0,0 +1,3 @@ +version=3 +opts=uversionmangle=s/^/0.0./ \ + http://sf.net/gasic/gasic_(r[0-9]+)\.(?:tgz|tar\.gz|tar\.xz|tar\.bz2) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/gasic.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
