# HG changeset patch
# User alermine
# Date 1352891044 18000
# Node ID 0b8b39c2ce0164df1e81ba202d3dd20d19a2f6fa
# Parent  1c699789d6d3c8460316121f82f88079c1fd465e
Uploaded

diff -r 1c699789d6d3 -r 0b8b39c2ce01 [APliBio]Nebula tools suite/README
--- a/[APliBio]Nebula tools suite/README	Wed Nov 14 06:02:48 2012 -0500
+++ b/[APliBio]Nebula tools suite/README	Wed Nov 14 06:04:04 2012 -0500
@@ -14,21 +14,28 @@
  - 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))
+ - 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
 
-1. Create symbolic links for FindPeaks & ChIPMunk:
+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) !! 
 
-2. Stop Galaxy
+5. Edit Galaxy universe_wsgi.ini file to provide a tool runner (in Tool Job Runners section)
+
+6. Stop Galaxy
 
-3. Make sure your Galaxy user source the environement like in the env.sh file
+7. Make sure your Galaxy user source the environement like in the env.sh file
 
-4. Start Galaxy
+8. Start Galaxy