[med-svn] [physamp] 02/02: Initial Debian packaging
Andreas Tille
tille at debian.org
Sat Aug 13 06:13:44 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository physamp.
commit be31016580d320c7f03de6b9f394f69b8431d837
Author: Andreas Tille <tille at debian.org>
Date: Sat Aug 13 08:12:55 2016 +0200
Initial Debian packaging
---
debian/changelog | 5 +++++
debian/clean | 2 ++
debian/compat | 1 +
debian/control | 33 +++++++++++++++++++++++++++++++++
debian/copyright | 26 ++++++++++++++++++++++++++
debian/examples | 1 +
debian/rules | 9 +++++++++
debian/source/format | 1 +
debian/tests/control | 3 +++
debian/tests/run-unit-test | 27 +++++++++++++++++++++++++++
debian/watch | 3 +++
11 files changed, 111 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..c13a125
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+physamp (0.2.0-1) UNRELEASED; urgency=medium
+
+ * Initial release (Closes: #???)
+
+ -- Andreas Tille <tille at debian.org> Wed, 27 Apr 2016 15:59:57 +0200
diff --git a/debian/clean b/debian/clean
new file mode 100644
index 0000000..8e4ca09
--- /dev/null
+++ b/debian/clean
@@ -0,0 +1,2 @@
+man/bppalnoptim.1.gz
+doc/physamp.info
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..6139942
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,33 @@
+Source: physamp
+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-dev (>= 2.2.0)
+Standards-Version: 3.9.8
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/physamp.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/physamp.git
+Homepage: http://biopp.univ-montp2.fr/forge/physamp
+
+Package: physamp
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
+Description: sample sequence alignment according to its corresponding phylogenetic tree
+ The PhySamp package currently contains one program, bppalnoptim, which
+ samples a sequence alignment by removing sequences in order to maximize
+ the number of sites suitable for a given analysis. The program has three
+ running modes:
+ * Interactive: the user will be iteratively proposed a set of choices
+ for sequence removal, with their corresponding site gains. The
+ procedure stops when the user does not want to remove more sequences,
+ and the resulting filtered alignment is written.
+ * Automatic: the user enters an a priori criterion for stopping
+ the filtering procedure (for instance a minimum number of
+ sequences to keep).
+ * Diagnostic: this mode allows one to plot the trade-off curve, by showing
+ the site gain as a function of the number of removed sequences.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..f6de8b6
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,26 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: PhySamp
+Upstream-Contact: Julien Dutheil <julien.dutheil at univ-montp2.fr>
+Source: http://biopp.univ-montp2.fr/repos/sources/physamp
+
+Files: *
+Copyright: 2014-2015 Julien Dutheil <julien.dutheil at univ-montp2.fr>
+License: GPL-3+
+
+Files: debian/*
+Copyright: 2016 Andreas Tille <tille at debian.org>
+License: GPL-3+
+
+License: GPL-3+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+ .
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ On Debian systems you can find the full text of the General Public
+ License version 3 at /usr/share/common-licenses/GPL-3.
diff --git a/debian/examples b/debian/examples
new file mode 100644
index 0000000..e39721e
--- /dev/null
+++ b/debian/examples
@@ -0,0 +1 @@
+examples/*
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..cd7793e
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,9 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+
+# export DEB_BUILD_MAINT_OPTIONS = hardening=+all # does not build
+export DEB_BUILD_MAINT_OPTIONS = hardening=+bindnow
+
+%:
+ dh $@
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/tests/control b/debian/tests/control
new file mode 100644
index 0000000..d2aa55a
--- /dev/null
+++ b/debian/tests/control
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr
diff --git a/debian/tests/run-unit-test b/debian/tests/run-unit-test
new file mode 100644
index 0000000..1c679eb
--- /dev/null
+++ b/debian/tests/run-unit-test
@@ -0,0 +1,27 @@
+#!/bin/bash
+set -e
+
+pkg="physamp"
+
+if [ "$AUTOPKGTEST_TMP" = "" ] ; then
+ AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+ trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cp -a /usr/share/doc/${pkg}/examples/PF01049/* $AUTOPKGTEST_TMP
+
+cd $AUTOPKGTEST_TMP
+find . -name "*.gz" -exec gunzip \{\} \;
+
+bppalnoptim param=AlnOptimFasttree.bpp
+bppalnoptim param=AlnOptimAuto.bpp LINKAGE=complete
+bppalnoptim param=AlnOptimAuto.bpp LINKAGE=single
+bppalnoptim param=AlnOptimAuto.bpp LINKAGE=average
+bppalnoptim param=AlnOptimAuto.bpp LINKAGE=median
+bppalnoptim param=AlnOptimAuto.bpp LINKAGE=centroid
+bppalnoptim param=AlnOptimAuto.bpp LINKAGE=ward
+
+#Get a selection of sequences:
+bppalnoptim param=AlnOptimFasttreeStop.bpp
+
+echo "PASS"
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..c4e27e7
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,3 @@
+version=3
+
+http://biopp.univ-montp2.fr/repos/sources/physamp physamp-(\d[-\d.]+)\.tar\.gz
--
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