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1 #RSAT tools - developed by Jocelyn Brayet <jocelyn.brayet@curie.fr>
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2 #Copyright (C) 2015 Institut Curie
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3 #
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4 #Programs are free software: you can redistribute it and/or modify
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5 #it under the terms of the GNU General Public License as published by
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6 #the Free Software Foundation, either version 3 of the License, or
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7 #(at your option) any later version.
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8 #
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9 #Programs are distributed in the hope that it will be useful,
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10 #but WITHOUT ANY WARRANTY; without even the implied warranty of
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11 #MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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12 #GNU General Public License for more details.
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13 #
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14 #You should have received a copy of the GNU General Public License
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15 #along with this program. If not, see <http://www.gnu.org/licenses/>.
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16 #
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17 ###########################################################'
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18
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19 1/ Additional softwares
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20
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21 -> Python packages :
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22
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23 - argparse
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24 - os
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25 - urllib
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26 - zipfile
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27 - time
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28 - platform
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29 - suds
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30
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31 ###########################################################'
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32
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33 2/ Recup organisms on each RSAT server :
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34
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35 To use -organism option in different tools, you must create organisms files for each RSAT server.
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36 Run supported-organisms_soap.py script with a terminal :
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37
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38 python supported-organisms_soap.py -f tab -galaxyPath /path/to/galaxy/tool-data
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39
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40 -> galaxyPath must be your tool-data path in your system
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41
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42 If you want help :
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43
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44 python supported-organisms_soap.py -h
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45
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46 ###########################################################'
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47
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46
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48 3/ Recup motif databases on each RSAT server :
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49
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50 To use -motif_db option peak motifs, you must create motif databases files for each RSAT server.
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51 Run supported-motif-databases_soap.py script with a terminal :
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52
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53 python supported-motif-databases_soap.py -galaxyPath /path/to/galaxy/tool-data
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54
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55 -> galaxyPath must be your tool-data path in your system
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56
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57 If you want help :
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58
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59 python supported-motif-databases_soap.py -h
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60
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61 ###########################################################'
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62
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63 4/ Display
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64
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65 If you want an aesthetical display, change "sanitize_all_html" parameter in galaxi.ini file.
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66 You must put : sanitize_all_html=False
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