Mercurial > repos > alermine > nebula
diff [APliBio]Nebula tools suite/README @ 0:2ec3ba0e9e70 draft
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| author | alermine |
|---|---|
| date | Thu, 25 Oct 2012 08:18:25 -0400 |
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| children | 0b8b39c2ce01 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/[APliBio]Nebula tools suite/README Thu Oct 25 08:18:25 2012 -0400 @@ -0,0 +1,34 @@ +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