Mercurial > repos > alermine > nebula
view [APliBio]Nebula tools suite/README @ 1:0ec82f1785af draft
Uploaded
author | alermine |
---|---|
date | Wed, 14 Nov 2012 05:59:25 -0500 |
parents | 2ec3ba0e9e70 |
children | 0b8b39c2ce01 |
line wrap: on
line source
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