Mercurial > repos > alermine > nebula
changeset 4:0b8b39c2ce01 draft default tip
Uploaded
author | alermine |
---|---|
date | Wed, 14 Nov 2012 06:04:04 -0500 |
parents | 1c699789d6d3 |
children | |
files | [APliBio]Nebula tools suite/README |
diffstat | 1 files changed, 13 insertions(+), 6 deletions(-) [+] |
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--- 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