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#RSAT tools - developed by Jocelyn Brayet <[e-mail]>
#Copyright (C) 2015  Institut Curie
#
#Programs are 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.
#
#Programs are 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/>.
#
###########################################################'

1/ Additional softwares

-> Python packages :

	- argparse
	- os
	- urllib
	- zipfile
	- time
	- platform
	- suds

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2/ Recup organisms on each RSAT server :

To use -organism option in different tools, you must create organisms files for each RSAT server. 
Run supported-organisms_soap.py script with a terminal :

	python supported-organisms_soap.py -f tab -galaxyPath /path/to/galaxy/tool-data

		-> galaxyPath must be your tool-data path in your system 

If you want help :

	python supported-organisms_soap.py -h

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3/ Recup motif databases on each RSAT server :

To use -motif_db option peak motifs, you must create motif databases files for each RSAT server. 
Run supported-motif-databases_soap.py script with a terminal :

	python supported-motif-databases_soap.py -galaxyPath /path/to/galaxy/tool-data

		-> galaxyPath must be your tool-data path in your system 

If you want help :

	python supported-motif-databases_soap.py -h

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4/ Display

If you want an aesthetical display, change "sanitize_all_html" parameter in galaxi.ini file. 
You must put : sanitize_all_html=False