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1 Copyleft ↄ⃝ 2012 Institut Curie
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2 Author(s): Valentina Boeva, Alban Lermine (Institut Curie) 2012
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3 Contact: valentina.boeva@curie.fr, alban.lermine@curie.fr
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4 This software is distributed under the terms of the GNU General
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5 Public License, either Version 2, June 1991 or Version 3, June 2007.
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6
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7 #################################################################
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8 ### INTEGRATION OF NEBULA TOOLS IN YOUR LOCAL GALAXY INSTANCE ###
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9 #################################################################
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10
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11 Requires:
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12
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13 - Perl installed on system
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14 - R installed on system
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15 - Samtools installed on system (http://sourceforge.net/projects/samtools/files/)
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16 - BedTools installed on system (http://code.google.com/p/bedtools/downloads/list)
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17 - FindPeaks installed on system (http://www.bcgsc.ca/platform/bioinfo/software/findpeaks)
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18 - ChipMunk 2 installed on system (http://autosome.ru/smbsm/librettos/libretto_chipmunk/chipmunk_downloads.rhtml |chipmunk_v2_scripts.zip v2.0 (NEW) supplementary ruby-scripts (see readme inside))
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19
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20 Step to installation:
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21
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22
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23 1. Create symbolic links for FindPeaks & ChIPMunk:
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24
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25 - ln -s /path/to/findpeaks/installation/jars/fp4 $GALAXY_INSTALL/galaxy-dist/tool-data/shared/jars/FindPeaks
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26 - ln -s /path/to/ChIPMunk/installation/ $GALAXY_INSTALL/galaxy-dist/tool-data/shared/jars/ChIPMunk
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27
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28 !! Respect the symbolic links names (FindPeaks & ChIPMunk) !!
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29
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30 2. Stop Galaxy
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31
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32 3. Make sure your Galaxy user source the environement like in the env.sh file
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33
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34 4. Start Galaxy
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