[med-svn] r14358 - in trunk/packages/aevol/trunk: . debian debian/source
David Parsons
dparsons-guest at alioth.debian.org
Wed Aug 7 09:51:44 UTC 2013
Author: dparsons-guest
Date: 2013-08-07 09:51:44 +0000 (Wed, 07 Aug 2013)
New Revision: 14358
Added:
trunk/packages/aevol/trunk/debian/
trunk/packages/aevol/trunk/debian/aevol.manpages
trunk/packages/aevol/trunk/debian/aevol_create.1
trunk/packages/aevol/trunk/debian/aevol_modify.1
trunk/packages/aevol/trunk/debian/aevol_propagate.1
trunk/packages/aevol/trunk/debian/aevol_run.1
trunk/packages/aevol/trunk/debian/aevol_run_X11.1
trunk/packages/aevol/trunk/debian/changelog
trunk/packages/aevol/trunk/debian/compat
trunk/packages/aevol/trunk/debian/control
trunk/packages/aevol/trunk/debian/copyright
trunk/packages/aevol/trunk/debian/docs
trunk/packages/aevol/trunk/debian/rules
trunk/packages/aevol/trunk/debian/source/
trunk/packages/aevol/trunk/debian/source/format
trunk/packages/aevol/trunk/debian/upstream
trunk/packages/aevol/trunk/debian/watch
Log:
[svn-inject] Application des modifications Debian (4.1-1) pour le tronc
Property changes on: trunk/packages/aevol/trunk/debian
___________________________________________________________________
Added: mergeWithUpstream
+ 1
Added: trunk/packages/aevol/trunk/debian/aevol.manpages
===================================================================
--- trunk/packages/aevol/trunk/debian/aevol.manpages (rev 0)
+++ trunk/packages/aevol/trunk/debian/aevol.manpages 2013-08-07 09:51:44 UTC (rev 14358)
@@ -0,0 +1,5 @@
+debian/aevol_create.1
+debian/aevol_run.1
+debian/aevol_run_X11.1
+debian/aevol_modify.1
+debian/aevol_propagate.1
Added: trunk/packages/aevol/trunk/debian/aevol_create.1
===================================================================
--- trunk/packages/aevol/trunk/debian/aevol_create.1 (rev 0)
+++ trunk/packages/aevol/trunk/debian/aevol_create.1 2013-08-07 09:51:44 UTC (rev 14358)
@@ -0,0 +1,34 @@
+.TH AEVOL "1" "August 2013" "aevol 4.1" "User Manual"
+.SH NAME
+aevol \- an in silico experimental evolution platform
+.SH SYNOPSIS
+.B aevol_create \-h
+or
+.B \-\-help
+.br
+.B aevol_create \-V
+or
+.B \-\-version
+.br
+.B aevol_create [\-f
+.I param_file]
+.SH DESCRIPTION
+.B Aevol
+is a simulation platform that allows to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome.
+.TP
+.B aevol_create
+create an experiment with setup as specified in
+.I param_file
+.SH OPTIONS
+.TP
+.B \-h, \-\-help
+print this help, then exit
+.TP
+.B \-V, \-\-version
+print version number, then exit
+.TP
+.B \-f, \-\-file
+.I param_file
+specify parameter file (default: param.in)
+.SH "SEE ALSO"
+.B aevol_run, aevol_modify, aevol_propagate
Added: trunk/packages/aevol/trunk/debian/aevol_modify.1
===================================================================
--- trunk/packages/aevol/trunk/debian/aevol_modify.1 (rev 0)
+++ trunk/packages/aevol/trunk/debian/aevol_modify.1 2013-08-07 09:51:44 UTC (rev 14358)
@@ -0,0 +1,39 @@
+.TH AEVOL "1" "August 2013" "aevol 4.1" "User Manual"
+.SH NAME
+aevol \- an in silico experimental evolution platform
+.SH SYNOPSIS
+.B aevol_modify \-h
+or
+.B \-\-help
+.br
+.B aevol_modify \-V
+or
+.B \-\-version
+.br
+.B aevol_modify \fR[\fB\-g\fI GENERATION\fR] \fR[\fB\-f\fI param_file\fR]
+.SH DESCRIPTION
+.B Aevol
+is a simulation platform that allows to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome.
+.TP
+.B aevol_modify
+modify an experiment as specified in
+.I param_file
+.SH OPTIONS
+.TP
+.B \-h, \-\-help
+print this help, then exit
+.TP
+.B \-V, \-\-version
+print version number, then exit
+.HP
+.B \-g, \-\-gener
+.I GENERATION
+.br
+specify generation number
+.HP
+.B \-f, \-\-file
+.I param_file
+.br
+specify parameter file (default: param.in)
+.SH "SEE ALSO"
+.B aevol_create, aevol_run, aevol_propagate
Added: trunk/packages/aevol/trunk/debian/aevol_propagate.1
===================================================================
--- trunk/packages/aevol/trunk/debian/aevol_propagate.1 (rev 0)
+++ trunk/packages/aevol/trunk/debian/aevol_propagate.1 2013-08-07 09:51:44 UTC (rev 14358)
@@ -0,0 +1,46 @@
+.TH AEVOL "1" "August 2013" "aevol 4.1" "User Manual"
+.SH NAME
+aevol \- an in silico experimental evolution platform
+.SH SYNOPSIS
+.B aevol_propagate \-h
+or
+.B \-\-help
+.br
+.B aevol_propagate \-V
+or
+.B \-\-version
+.br
+.B aevol_propagate \fR[\fB\-g\fI GENERATION\fR] \fR[\fB\-i\fI in_dir\fR] \fR[\fB\-o\fI out_dir\fR] \fR[\fB\-v\fR]
+.SH DESCRIPTION
+.B Aevol
+is a simulation platform that allows to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome.
+.TP
+.B aevol_propagate
+create a fresh copy of the experiment
+.SH OPTIONS
+.TP
+.B \-h, \-\-help
+print this help, then exit
+.TP
+.B \-V, \-\-version
+print version number, then exit
+.HP
+.B \-g, \-\-gener
+.I GENERATION
+.br
+specify generation number
+.HP
+.B \-i, \-\-in
+.I in_dir
+.br
+specify input directory (default ".")
+.HP
+.B \-o, \-\-out
+.I in_dir
+.br
+specify output directory (default "./output")
+.TP
+.B \-v, \-\-verbose
+be verbose
+.SH "SEE ALSO"
+.B aevol_create, aevol_run, aevol_modify
Added: trunk/packages/aevol/trunk/debian/aevol_run.1
===================================================================
--- trunk/packages/aevol/trunk/debian/aevol_run.1 (rev 0)
+++ trunk/packages/aevol/trunk/debian/aevol_run.1 2013-08-07 09:51:44 UTC (rev 14358)
@@ -0,0 +1,52 @@
+.TH AEVOL "1" "August 2013" "aevol 4.1" "User Manual"
+.SH NAME
+aevol \- an in silico experimental evolution platform
+.SH SYNOPSIS
+.B aevol_run_X11 \-h
+|
+.B \-\-help
+.br
+.B aevol_run_X11 \-V
+|
+.B \-\-version
+.br
+.B aevol_run_X11 \fR[\fB\-r\fI GENERATION\fR] \fR[\fB\-n\fI NB_GENER\fR] \fR[\fB\-tvwx\fR]
+.SH DESCRIPTION
+.B Aevol
+is a simulation platform that allows to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome.
+.TP
+.B aevol_run, aevol_run_X11
+run an aevol simulation.
+.SH OPTIONS
+.TP
+.B \-h, \-\-help
+print this help, then exit
+.TP
+.B \-V, \-\-version
+print version number, then exit
+.HP
+.B \-n, \-\-nbgener
+.I NB_GENER
+.br
+number of generations to be run
+.HP
+.B \-r, \-\-resume
+.I GENERATION
+.br
+resume simulation at given generation
+.TP
+.B \-t, \-\-text
+use text files instead of binary files when possible
+.TP
+.B \-v, \-\-verbose
+be verbose
+.TP
+.B \-w, \-\-wait
+pause after loading
+.TP
+.B \-x, \-\-noX
+don't display X outputs upon start
+.br
+send SIGUSR1 to switch X output on/off
+.SH "SEE ALSO"
+.B aevol_create, aevol_modify, aevol_propagate
Added: trunk/packages/aevol/trunk/debian/aevol_run_X11.1
===================================================================
--- trunk/packages/aevol/trunk/debian/aevol_run_X11.1 (rev 0)
+++ trunk/packages/aevol/trunk/debian/aevol_run_X11.1 2013-08-07 09:51:44 UTC (rev 14358)
@@ -0,0 +1 @@
+link aevol_run.1
\ No newline at end of file
Property changes on: trunk/packages/aevol/trunk/debian/aevol_run_X11.1
___________________________________________________________________
Added: svn:special
+ *
Added: trunk/packages/aevol/trunk/debian/changelog
===================================================================
--- trunk/packages/aevol/trunk/debian/changelog (rev 0)
+++ trunk/packages/aevol/trunk/debian/changelog 2013-08-07 09:51:44 UTC (rev 14358)
@@ -0,0 +1,5 @@
+aevol (4.1-1) unstable; urgency=low
+
+ * Initial release (Closes: #718887)
+
+ -- David Parsons <david.parsons at inria.fr> Mon, 05 Aug 2013 17:07:40 +0200
Added: trunk/packages/aevol/trunk/debian/compat
===================================================================
--- trunk/packages/aevol/trunk/debian/compat (rev 0)
+++ trunk/packages/aevol/trunk/debian/compat 2013-08-07 09:51:44 UTC (rev 14358)
@@ -0,0 +1 @@
+9
Added: trunk/packages/aevol/trunk/debian/control
===================================================================
--- trunk/packages/aevol/trunk/debian/control (rev 0)
+++ trunk/packages/aevol/trunk/debian/control 2013-08-07 09:51:44 UTC (rev 14358)
@@ -0,0 +1,25 @@
+Source: aevol
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: David Parsons <david.parsons at inria.fr>
+Build-Depends: debhelper (>= 9.0), zlib1g-dev, autotools-dev, libx11-dev
+Standards-Version: 3.9.4
+Homepage: http://www.aevol.fr/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/aevol/trunk/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/aevol/trunk/
+
+Package: aevol
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: A digital genetics model to run Evolution Experiments in silico
+ Aevol is a digital genetics model: populations of digital organisms are subjected to a process of selection and variation,
+ which creates a Darwinian dynamics.
+ By modifying the characteristics of selection (e.g. population size, type of environment, environmental variations)
+ or variation (e.g. mutation rates, chromosomal rearrangement rates, types of rearrangements, horizontal transfer),
+ one can study experimentally the impact of these parameters on the structure of the evolved organisms.
+ In particular, since Aevol integrates a precise and realistic model of the genome, it allows for the study of structural
+ variations of the genome (e.g. number of genes, synteny, proportion of coding sequences).
+ .
+ The simulation platform comes along with a set of tools for analysing phylogenies and measuring many characteristics of
+ the organisms and populations along evolution.
Added: trunk/packages/aevol/trunk/debian/copyright
===================================================================
--- trunk/packages/aevol/trunk/debian/copyright (rev 0)
+++ trunk/packages/aevol/trunk/debian/copyright 2013-08-07 09:51:44 UTC (rev 14358)
@@ -0,0 +1,49 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: aevol
+Source: <url://example.com>
+
+Files: *
+Copyright: 2003 - 2013 Guillaume Beslon
+ 2003 - 2013 Carole Knibbe
+ 2008 - 2013 David P. Parsons
+ 2003 - 2007 Virginie Mathivet
+ 2009 - 2013 Dusan Misevic
+ 2010 - 2013 Antoine Frénoy
+ 2011 - 2013 Bérénice Batut
+
+License: GPL-2+
+ This package 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 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 2 can be found in "/usr/share/common-licenses/GPL-2".
+
+Files: debian/*
+Copyright: 2013 David Parsons <david.parsons at inria.fr>
+License: GPL-2+
+ This package 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 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 2 can be found in "/usr/share/common-licenses/GPL-2".
+
\ No newline at end of file
Added: trunk/packages/aevol/trunk/debian/docs
===================================================================
--- trunk/packages/aevol/trunk/debian/docs (rev 0)
+++ trunk/packages/aevol/trunk/debian/docs 2013-08-07 09:51:44 UTC (rev 14358)
@@ -0,0 +1,2 @@
+NEWS
+README
Added: trunk/packages/aevol/trunk/debian/rules
===================================================================
--- trunk/packages/aevol/trunk/debian/rules (rev 0)
+++ trunk/packages/aevol/trunk/debian/rules 2013-08-07 09:51:44 UTC (rev 14358)
@@ -0,0 +1,13 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+# Sample debian/rules that uses debhelper.
+# This file was originally written by Joey Hess and Craig Small.
+# As a special exception, when this file is copied by dh-make into a
+# dh-make output file, you may use that output file without restriction.
+# This special exception was added by Craig Small in version 0.37 of dh-make.
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+%:
+ dh $@ --with autotools-dev
Property changes on: trunk/packages/aevol/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/aevol/trunk/debian/source/format
===================================================================
--- trunk/packages/aevol/trunk/debian/source/format (rev 0)
+++ trunk/packages/aevol/trunk/debian/source/format 2013-08-07 09:51:44 UTC (rev 14358)
@@ -0,0 +1 @@
+3.0 (quilt)
Added: trunk/packages/aevol/trunk/debian/upstream
===================================================================
--- trunk/packages/aevol/trunk/debian/upstream (rev 0)
+++ trunk/packages/aevol/trunk/debian/upstream 2013-08-07 09:51:44 UTC (rev 14358)
@@ -0,0 +1,49 @@
+Reference:
+ Author: Dusan Misevic and Antoine Frenoy and David P. Parsons and Francois Taddei
+ Title: "Effects of public good properties on the evolution of cooperation"
+ Booktitle: Proceedings of Artificial Life XIII
+ Year: 2012
+ Pages: 218-225
+ Eprint: http://mitpress.mit.edu/sites/default/files/titles/content/alife13/978-0-262-31050-5-ch030.pdf
+ URL: http://www.aevol.fr/publications/
+ Type: inproceedings
+
+ Author: Antoine Frenoy and Francois Taddei and Dusan Misevic
+ Title: "Robustness and evolvability of cooperation"
+ Booktitle: Proceedings of Artificial Life XIII
+ Year: 2012
+ Pages: 53-58
+ Eprint: http://mitpress.mit.edu/sites/default/files/titles/content/alife13/978-0-262-31050-5-ch008.pdf
+ URL: http://www.aevol.fr/publications/
+ Type: inproceedings
+
+ Author: Guillaume Beslon and David P. Parsons and Yolanda Sanchez-Dehesa and Jose Maria Pena and Carole Knibbe
+ Title: "Scaling Laws in Bacterial Genomes: A Side-Effect of Selection of Mutational Robustness"
+ Journal: BioSystems
+ Year: 2010
+ Volume: 102
+ Number: 1
+ Pages: 32-40
+ URL: http://www.aevol.fr/publications/
+ Type: article
+
+ Author: David P. Parsons and Carole Knibbe and Guillaume Beslon
+ Title: "Importance of the rearrangement rates on the organization of transcription"
+ Booktitle: Proceedings of Artificial Life XII
+ Year: 2010
+ Pages: 479-486
+ Eprint: http://mitpress.mit.edu/sites/default/files/titles/alife/0262290758chap92.pdf
+ URL: http://www.aevol.fr/publications/
+ Type: inproceedings
+
+ Author: Carole Knibbe and Antoine Coulon and Olivier Mazet and Jean-Michel Fayard and Guillaume Beslon
+ Title: "A long-term evolutionary pressure on the amount of noncoding DNA"
+ Journal: Mol. Biol. Evol.
+ Year: 2007
+ Volume: 24
+ Number: 10
+ Pages: 2344-2353
+ Eprint: http://mbe.oxfordjournals.org/content/24/10/2344.full.pdf+html?sid=9a6ee107-7aed-4750-8015-f8a2cc136cf9
+ URL: http://www.aevol.fr/publications/
+ Type: article
+
\ No newline at end of file
Added: trunk/packages/aevol/trunk/debian/watch
===================================================================
--- trunk/packages/aevol/trunk/debian/watch (rev 0)
+++ trunk/packages/aevol/trunk/debian/watch 2013-08-07 09:51:44 UTC (rev 14358)
@@ -0,0 +1,2 @@
+version=3
+http://www.aevol.fr/download/index.php http://gforge.liris.cnrs.fr/frs/download.php/.*/aevol-(.*)\.(?:tar(?:\.gz|\.bz2)?|tgz|zip)
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