view README @ 51:b60e0f0dab74 draft default tip

another try at adding amigo tool

Welcome to OBO Tool Repository for BBOP Galaxy
 
The following libraries need to be installed to use the obo tools:

# termfinder needs g++ and other build tools
sudo apt-get $APT_OPTS install build-essential

# perl dbi / perl DBD::mysql 
sudo apt-get $APT_OPTS install libdbi-perl libdbd-mysql-perl

# GO:TermFinder needs dependencies GraphViz and GD graphics libraries 
sudo apt-get $APT_OPTS install libgraphviz-perl
sudo apt-get $APT_OPTS install libgd-gd2-perl

# subversion for retrieving versioned gene ontologies
sudo apt-get $APT_OPTS install subversion

--- Term Enrichment related ---
(currently used - heavily tied to mysql / old data model)
http://geneontology.svn.sourceforge.net/viewvc/geneontology/go-dev/trunk/amigo/amigo/cgi-bin/term_enrichment?view=log

(command line version - file based)
http://geneontology.svn.sourceforge.net/viewvc/geneontology/go-dev/trunk/go-db-perl/

http://geneontology.svn.sourceforge.net/viewvc/geneontology/go-dev/trunk/go-db-perl/scripts/go-find-enriched-terms.pl?view=log

--- Gene Associations ---
svn --ignore-externals co svn://ext.geneontology.org/trunk/gene-associations gene-associations

--- AmiGO related ---

for AmiGO Manual 
http://wiki.geneontology.org/index.php/AmiGO_Manual:_Visualize

online tool to play around (current version, has R Wrapper ramigo)
http://amigo.geneontology.org/cgi-bin/amigo/visualize?mode=client

online tool Amigo2
http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo?mode=visualize

entry point Amigo2
https://github.com/kltm/amigo/blob/master/perl/bin/visualize

--- workflows ---

gene set + ontology + gene associations =

gene products + background set = (good) + (ambiguous) + (no match, missing)