[med-svn] [pipasic] 02/02: Add initial debian/ packaging
Andreas Tille
tille at debian.org
Tue Sep 29 13:41:32 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository pipasic.
commit ba43882ba2e2b75c238589fc757b2d386d0d84f2
Author: Andreas Tille <tille at debian.org>
Date: Tue Sep 29 15:29:23 2015 +0200
Add initial debian/ packaging
---
debian/bin/pipasic | 2 ++
debian/changelog | 5 +++++
debian/compat | 1 +
debian/control | 37 +++++++++++++++++++++++++++++++++++++
debian/copyright | 11 +++++++++++
debian/get-orig-source | 33 +++++++++++++++++++++++++++++++++
debian/install | 3 +++
debian/links | 1 +
debian/rules | 8 ++++++++
debian/source/format | 1 +
debian/upstream/metadata | 12 ++++++++++++
debian/watch | 1 +
12 files changed, 115 insertions(+)
diff --git a/debian/bin/pipasic b/debian/bin/pipasic
new file mode 100644
index 0000000..17814f3
--- /dev/null
+++ b/debian/bin/pipasic
@@ -0,0 +1,2 @@
+#!/bin/sh
+python /usr/share/pipasic/pipasic.py
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..35458b7
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+pipasic (0.0+15-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org> Tue, 29 Sep 2015 15:21:50 +0200
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..8101070
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,37 @@
+Source: pipasic
+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: 3.9.6
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/pipasic.git
+Vcs-Git: git://anonscm.debian.org/debian-med/pipasic.git
+Homepage: http://sourceforge.net/projects/pipasic/
+
+Package: pipasic
+Architecture: any
+Depends: ${python:Depends},
+ ${misc:Depends},
+ python-biopython,
+ python-numpy,
+ python-matplotlib
+Description: Protein Abundance Correction in Metaproteomic Data
+ Metaproteomic analysis allows studying the interplay of organisms or
+ functional groups and has become increasingly popular also for
+ diagnostic purposes. However, difficulties arise due to the high
+ sequence similarity between related organisms. Further, the state of
+ conservation of proteins between species can be correlated with their
+ expression level which can lead to significant bias in results and
+ interpretation. These challenges are similar but not identical to the
+ challenges arising in the analysis of metagenomic samples and require
+ specific solutions.
+ .
+ pipasic (peptide intensity-weighted proteome abundance similarity
+ correction) is a tool which corrects identification and spectral
+ counting based quantification results using peptide similarity
+ estimation and expression level weighting within a non-negative lasso
+ framework. pipasic has distinct advantages over approaches only
+ regarding unique peptides or aggregating results to the lowest common
+ ancestor.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..c76e73d
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,11 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: <pkg>
+Source: <path_to_download>
+
+Files: *
+Copyright: © 20xx-20yy <upstream>
+License: <license>
+
+Files: debian/*
+Copyright: © 2014 maintainername <maintainer at e.mail>
+License: <license>
diff --git a/debian/get-orig-source b/debian/get-orig-source
new file mode 100755
index 0000000..d44ea3e
--- /dev/null
+++ b/debian/get-orig-source
@@ -0,0 +1,33 @@
+#!/bin/sh
+# if you need to repack for whatever reason you can
+# use this script via uscan or directly
+#
+# FIXME: currently the code is not conform to Debian Policy
+# http://www.debian.org/doc/debian-policy/ch-source.html
+# "get-orig-source (optional)"
+# This target may be invoked in any directory, ...
+# --> currently it is assumed the script is called in the
+# source directory featuring the debian/ dir
+
+COMPRESS=xz
+
+set -e
+NAME=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'`
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ { print $2 }' | sed 's/\([0-9\.]\+\)-[0-9]\+$/\1/'`
+
+## NO tags no branches
+SVNURI="svn://svn.code.sf.net/p/pipasic/code/trunk"
+revision=`LANG=C svn info ${SVNURI} | grep "^Last Changed Rev:" | sed 's/Last Changed Rev: *//'`
+VERSION=`echo ${VERSION}| sed "s/+[0-9]\+$//"`+${revision}
+
+TARDIR=${NAME}-${VERSION}
+
+mkdir -p ../tarballs
+cd ../tarballs
+# svn export conserves time stamps of the files, checkout does not
+LC_ALL=C svn export ${SVNURI} ${TARDIR} >/dev/null 2>/dev/null || true
+
+find ${TARDIR} -type f -exec chmod 644 \{\} \;
+
+GZIP="--best --no-name" tar --owner=root --group=root --mode=a+rX -caf "$NAME"_"$VERSION".orig.tar.${COMPRESS} "${TARDIR}"
+rm -rf ${TARDIR}
diff --git a/debian/install b/debian/install
new file mode 100644
index 0000000..4a780e8
--- /dev/null
+++ b/debian/install
@@ -0,0 +1,3 @@
+*.py usr/share/pipasic
+config_files/* etc/pipasic
+debian/bin usr
diff --git a/debian/links b/debian/links
new file mode 100644
index 0000000..723bfd4
--- /dev/null
+++ b/debian/links
@@ -0,0 +1 @@
+etc/pipasic usr/share/pipasic/config_files
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..7d11dde
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,8 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+
+DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
+
+%:
+ dh $@ --with python2
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/metadata b/debian/upstream/metadata
new file mode 100644
index 0000000..0400573
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,12 @@
+Reference:
+ Author: Anke Penzlin and Martin S. Lindner and Joerg Doellinger and Piotr Wojtek Dabrowski and Andreas Nitsche and Bernhard Y. Renard
+ Title: "Pipasic: similarity and expression correction for strain-level identification and quantification in metaproteomics"
+ Journal: Bioinformatics
+ Year: 2014
+ Volume: 30
+ Number: 12
+ Pages: i149–i156
+ DOI: 10.1093/bioinformatics/btu267
+ PMID: 24931978
+ URL: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4058918/
+ eprint: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4058918/pdf/btu267.pdf
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..cf22602
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1 @@
+# There is no tarball download location, libMuscle is only available in SVN
--
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