[med-svn] [gasic] 01/01: Add some initial debian/ dir
Andreas Tille
tille at debian.org
Sat Feb 8 08:23:10 UTC 2014
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 <tille at debian.org>
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 <tille at debian.org> 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 <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>
+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 <LindnerM at rki.de>
+Source: http://sourceforge.net/projects/gasic/files/
+
+Files: *
+Copyright: 2ß12-2013 Martin S. Lindner <LindnerM at rki.de>
+ Robert Koch-Institut
+License: BSDlike
+
+Files: debian/*
+Copyright: 2014 Andreas Tille <tille at 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.
+
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)
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