[med-svn] [jmodeltest] 02/02: Add initial Debian packaging
Andreas Tille
tille at debian.org
Mon Oct 19 15:12:35 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository jmodeltest.
commit 934e38211a2ea93c639597913093d2a1bba9f55b
Author: Andreas Tille <tille at debian.org>
Date: Mon Oct 19 17:10:34 2015 +0200
Add initial Debian packaging
---
debian/changelog | 5 +++++
debian/compat | 1 +
debian/control | 34 ++++++++++++++++++++++++++++++++++
debian/copyright | 39 +++++++++++++++++++++++++++++++++++++++
debian/rules | 14 ++++++++++++++
debian/source/format | 1 +
debian/upstream/metadata | 11 +++++++++++
debian/watch | 4 ++++
8 files changed, 109 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..9d91ce5
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+jmodeltest (2.1.7-20150220+dfsg-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org> Thu, 27 Aug 2015 14:20:26 +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..bb2f4da
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,34 @@
+Source: jmodeltest
+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),
+ alter-sequence-alignment,
+ libfreemarker-java,
+ libjcommon-java,
+ libjfreechart-java,
+ libmpj-java,
+ libpal-java,
+ prottest
+Standards-Version: 3.9.6
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/jmodeltest.git
+Vcs-Git: git://anonscm.debian.org/debian-med/jmodeltest.git
+Homepage: https://code.google.com/p/jmodeltest2/
+
+Package: jmodeltest
+Architecture: all
+Depends: ${misc:Depends},
+ ${java:Depends}
+Description: HPC selection of models of nucleotide substitution
+ jModelTest is a tool to carry out statistical selection of best-fit
+ models of nucleotide substitution. It implements five different model
+ selection strategies: hierarchical and dynamical likelihood ratio tests
+ (hLRT and dLRT), Akaike and Bayesian information criteria (AIC and BIC),
+ and a decision theory method (DT). It also provides estimates of model
+ selection uncertainty, parameter importances and model-averaged
+ parameter estimates, including model-averaged tree topologies.
+ jModelTest 2 includes High Performance Computing (HPC) capabilities and
+ additional features like new strategies for tree optimization, model-
+ averaged phylogenetic trees (both topology and branch lenght), heuristic
+ filtering and automatic logging of user activity.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..cacdc0a
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,39 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: jModelTest
+Upstream-Contact: Diego Darriba <diegodl84 at gmail.com>
+Source: https://github.com//ddarriba/jmodeltest2/releases
+Files-Excluded: exe/phyml
+ extra/mpj.tar.gz
+ */alter.jar
+ */freemarker.jar
+ */jcommon-*.jar
+ */jfreechart-*.jar
+ */mpj.jar
+ */pal.jar
+ */prottest-*.jar
+ jModelTest.jar
+
+Files: *
+Copyright: 2008-2015 Diego Darriba <diegodl84 at gmail.com>
+ Guillermo L. Taboada <taboada at udc.es>
+ Ramón Doallo <doallo at udc.es>
+ David Posada <dposada at uvigo.es)>
+License: GPL-2+
+
+Files: debian/*
+Copyright: 2015 Andreas Tille <tille at debian.org>
+License: GPL-2+
+
+License: GPL-2+
+ 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 2 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 systms you can find the full text of the GNU General Public
+ License at /usr/share/common-licenses/GPL-2.
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..9b4b557
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,14 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+JAVA_HOME=/usr/lib/jvm/default-java
+
+%:
+ dh $@ --with javahelper
+
+get-orig-source:
+ uscan --verbose --force-download --repack --compression xz
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..3764b08
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,11 @@
+Reference:
+ Author: Diego Darriba and Guillermo L Taboada and Ramón Doallo and David Posada
+ Title: "jModelTest 2: more models, new heuristics and parallel computing"
+ Journal: Nature Methods
+ Year: 2012
+ Volume: 9
+ Number: 8
+ Pages: 772
+ DOI: 10.1038/nmeth.2109
+ PMID: 22847109
+ URL: http://www.nature.com/nmeth/journal/v9/n8/full/nmeth.2109.html
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..6a70f44
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,4 @@
+version=3
+
+opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g" \
+ https://github.com//ddarriba/jmodeltest2/releases .*/archive/jModelTest-(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
--
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