[med-svn] [maffilter] 02/02: Add initial Debian packaging
Andreas Tille
tille at debian.org
Thu Apr 14 09:06:26 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository maffilter.
commit 6b4afad7a1db017a89283b028dd569f63c80c869
Author: Andreas Tille <tille at debian.org>
Date: Thu Apr 14 11:04:07 2016 +0200
Add initial Debian packaging
---
debian/changelog | 5 +++++
debian/compat | 1 +
debian/control | 37 +++++++++++++++++++++++++++++++++++
debian/copyright | 50 ++++++++++++++++++++++++++++++++++++++++++++++++
debian/manpages | 1 +
debian/rules | 20 +++++++++++++++++++
debian/source/format | 1 +
debian/upstream/metadata | 11 +++++++++++
debian/watch | 4 ++++
9 files changed, 130 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..ed36151
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+maffilter (1.1.0-1+dfsg-1) UNRELEASED; urgency=medium
+
+ * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org> Wed, 06 Apr 2016 12:27:55 +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..ba79ce9
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,37 @@
+Source: maffilter
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>,
+ Julien Dutheil <julien.dutheil at univ-montp2.fr>
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 9),
+ cmake,
+ texinfo,
+ libbpp-phyl-omics-dev (>= 2.2.0),
+ libboost-iostreams-dev (>= 1.54.0),
+ libzip2,
+ libbz2-1.0
+Standards-Version: 3.9.8
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/maffilter.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/maffilter.git
+Homepage: http://biopp.univ-montp2.fr/forge/maffilter
+
+Package: maffilter
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
+Description: process genome alignment in the Multiple Alignment Format
+ MafFilter applies a series of "filters" to a MAF file, in order to
+ clean it, extract data and computer statistics while keeping track of
+ the associated meta-data such as genome coordinates and quality scores.
+ .
+ * It can process the alignment to remove low-quality / ambiguous /
+ masked regions.
+ * It can export data into a single or multiple alignment file in
+ format such as Fasta or Clustal.
+ * It can read annotation data in GFF or GTF format, and extract the
+ corresponding alignment.
+ * It can perform sliding windows calculations.
+ * It can reconstruct phylogeny/genealogy along the genome alignment.
+ * It can compute population genetics statistics, such as site
+ frequency spectrum, number of fixed/polymorphic sites, etc.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..2f2e6ae
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,50 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: MafFilter
+Upstream-Contact: Julien Dutheil <julien.dutheil at univ-montp2.fr>
+Source: http://biopp.univ-montp2.fr/repos/sources/maffilter/
+Files-Excluded: *.log
+ *.ps.raw
+ */debian
+
+Files: *
+Copyright: 2014-2016 Julien Dutheil <julien.dutheil at univ-montp2.fr>
+ Sylvain Gaillard <sylvain.gaillard at angers.inra.fr>
+ Eva Stukenbrock <eva.stukenbrock at mpi-marburg.mpg.de>
+License: CeCILL
+
+Files: debian/*
+Copyright: 2014 Julien Dutheil <julien.dutheil at univ-montp2.fr>
+ 2016 Andreas Tille <tille at debian.org>
+License: CeCILL
+
+License: CeCILL
+ The provided software is distributed under the CeCILL license:
+ .
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+ .
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+ .
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+ .
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+ .
+ The complete text of the license may be found here:
+ http://www.cecill.info/licences/Licence_CeCILL_V2-en.html
diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..1b82e58
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+man/maffilter.1.gz
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..b340142
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,20 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+
+# some helpful variables - uncomment them if needed
+# shamelessly stolen from http://jmtd.net/log/awk/
+#DEBVERS := $(shell dpkg-parsechangelog | awk '/^Version:/ {print $$2}')
+#VERSION := $(shell echo '$(DEBVERS)' | sed -e 's/^[0-9]*://' -e 's/-.*//')
+#DEBFLAVOR := $(shell dpkg-parsechangelog | awk '/^Distribution:/ {print $$2}')
+#DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
+#DEBIAN_BRANCH := $(shell awk 'BEGIN{FS="[= ]+"} /debian-branch/ {print $$2}' debian/gbp.conf)
+#GIT_TAG := $(subst ~,_,$(VERSION))
+
+# alternatively to manually set those variables, you can
+# include /usr/share/dpkg/default.mk
+# and use what is set there.
+
+%:
+ dh $@
+
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..3491cca
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,11 @@
+Reference:
+ Author: Julien Y Dutheil and Sylvain Gaillard and Eva H Stukenbrock
+ Title: "MafFilter: a highly flexible and extensible multiple genome alignment files processor"
+ Journal: BMC Genomics
+ Year: 2014
+ Volume: 15
+ Pages: 53
+ DOI: 10.1186/1471-2164-15-53
+ PMID: 24447531
+ URL: http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-15-53
+ eprint: http://bmcgenomics.biomedcentral.com/track/pdf/10.1186/1471-2164-15-53?site=bmcgenomics.biomedcentral.com
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..79a1743
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,4 @@
+version=3
+
+opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
+ http://biopp.univ-montp2.fr/repos/sources/maffilter/ [Mm]af[Ff]ilter-(\d[-\d.]+)\.tar\.gz
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