annotate [APliBio]Nebula tools suite/README @ 4:0b8b39c2ce01 draft default tip

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Copyleft ↄ⃝ 2012 Institut Curie
Author(s): Valentina Boeva, Alban Lermine (Institut Curie) 2012
Contact: [e-mail], [e-mail]
This software is distributed under the terms of the GNU General
Public License, either Version 2, June 1991 or Version 3, June 2007.

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### INTEGRATION OF NEBULA TOOLS IN YOUR LOCAL GALAXY INSTANCE ###
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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) | Available in Nebula_External directory
 - 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)) | Available in Nebula_External directory

Step to installation:

1. Copy/paste the Nebula directory in your $GALAXY_INSTALL/galaxy-dist/tools directory

2. Copy/paste the content of the tool_conf.abstract.xml in your $GALAXY_INSTALL/galaxy-dist/tool_conf.xml file

3. Copy/paste the chrom directory (in chrom.zip) in your $GALAXY_INSTALL/galaxy-dist/tool-data/shared/ucsc directory

4. 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) !! 

5. Edit Galaxy universe_wsgi.ini file to provide a tool runner (in Tool Job Runners section)

6. Stop Galaxy

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

8. Start Galaxy