[med-svn] [fitgpc] 02/02: Add initial debian/ dir
Andreas Tille
tille at debian.org
Fri Feb 7 16:00:13 UTC 2014
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository fitgpc.
commit ef9b9d27e82b26d1851f66cb3af42c64601bdc75
Author: Andreas Tille <tille at debian.org>
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 <tille at debian.org> 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 <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at 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.
+
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 <LindnerM at 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 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..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)
--
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