[med-svn] [indelible] 02/02: Added basic debian packaging files

[Fabian Klötzl]

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kloetzl-guest pushed a commit to branch master
in repository indelible.

commit ac17eaa253c4531f7640d051eede3582baf63f97
Author: Fabian Klötzl <fabian at kloetzl.info>
Date:   Wed Dec 9 15:54:58 2015 +0100

    Added basic debian packaging files
---
 debian/changelog         |  5 +++++
 debian/compat            |  1 +
 debian/control           | 34 ++++++++++++++++++++++++++++++++++
 debian/copyright         | 20 ++++++++++++++++++++
 debian/source/format     |  1 +
 debian/upstream/metadata | 12 ++++++++++++
 6 files changed, 73 insertions(+)

diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..6bc8089
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+indelible (1.03-1) UNRELEASED; urgency=medium
+
+  * Initial release. (Closes: #807486)
+
+ -- Fabian Klötzl <kloetzl at evolbio.mpg.de>  Wed, 09 Dec 2015 14:42:52 +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..98cdd78
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,34 @@
+Source: indelible
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Fabian Klötzl <kloetzl at evolbio.mpg.de>
+Build-Depends: debhelper (>= 9)
+Standards-Version: 3.9.6
+Vcs-Browser: http://anonscm.debian.org/cgit/debian-med/indelible.git/tree/
+Vcs-Git: git://anonscm.debian.org/debian-med/indelible.git
+Homepage: http://abacus.gene.ucl.ac.uk/software/indelible/
+
+Package: indelible
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: A powerful and flexible simulator of biological evolution
+ INDELible is a new, portable, and flexible application for biological
+ sequence simulation that combines many features in the same place for
+ the first time. Using a length-dependent model of indel formation it
+ can simulate evolution of multi-partitioned nucleotide, amino-acid,
+ or codon data sets through the processes of insertion, deletion, and
+ substitution in continuous time.
+ .
+ Nucleotide simulations may use the general unrestricted model or the
+ general time reversible model and its derivatives, and amino-acid
+ simulations can be conducted using fifteen different empirical rate
+ matrices. Substitution rate heterogeneity can be modelled via the
+ continuous and discrete gamma distributions, with or without a proportion
+ of invariant sites. INDELible can also simulate under non-homogenous
+ and non-stationary conditions where evolutionary models are permitted
+ to change across a phylogeny.
+ .
+ Unique among indel simulation programs, INDELible offers the ability
+ to simulate using codon models that exhibit nonsynonymous/synonymous
+ rate ratio heterogeneity among sites and/or lineages.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..f5b7299
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,20 @@
+Files: debian/*
+Copyright: © 2010 William Fletcher
+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 package 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.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 3 can be found in `/usr/share/common-licenses/GPL-3'.
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..e43ccbb
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,12 @@
+Reference:
+  Author: William Fletcher and Ziheng Yang
+  Title: "INDELible: A Flexible Simulator of Biological Sequence Evolution"
+  Journal: Molecular Biology and Evolution
+  Year: 2009
+  Volume: 26
+  Number: 8
+  Pages: 1879-1888
+  DOI: 10.1093/molbev/msp098
+  URL: http://mbe.oxfordjournals.org/content/26/8/1879.abstract
+  eprint: http://mbe.oxfordjournals.org/content/26/8/1879.full.pdf+html
+

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