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author alermine
date Wed, 14 Nov 2012 05:59:25 -0500
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Copyleft ↄ⃝ 2012 Institut Curie
Author(s): Valentina Boeva, Alban Lermine (Institut Curie) 2012
Contact: valentina.boeva@curie.fr, alban.lermine@curie.fr
This software is distributed under the terms of the GNU General
Public License, either Version 2, June 1991 or Version 3, June 2007.

#################################################################
### INTEGRATION OF NEBULA TOOLS IN YOUR LOCAL GALAXY INSTANCE ###
#################################################################

Requires:

 - Perl installed on system
 - R installed on system
 - Samtools installed on system (http://sourceforge.net/projects/samtools/files/)
 - BedTools installed on system (http://code.google.com/p/bedtools/downloads/list)
 - FindPeaks installed on system (http://www.bcgsc.ca/platform/bioinfo/software/findpeaks)
 - 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))

Step to installation:


1. Create symbolic links for FindPeaks & ChIPMunk:

	- ln -s /path/to/findpeaks/installation/jars/fp4 $GALAXY_INSTALL/galaxy-dist/tool-data/shared/jars/FindPeaks
	- ln -s /path/to/ChIPMunk/installation/ $GALAXY_INSTALL/galaxy-dist/tool-data/shared/jars/ChIPMunk

!! Respect the symbolic links names (FindPeaks & ChIPMunk) !! 

2. Stop Galaxy

3. Make sure your Galaxy user source the environement like in the env.sh file

4. Start Galaxy