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 <[email protected]> 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 <[email protected]> +Uploaders: David Parsons <[email protected]> +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 Fr�noy + 2011 - 2013 B�r�nice 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 <[email protected]> +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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