diff README @ 0:028babd7a6c5 draft default tip

Try at a fresh start...

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README	Fri Mar 29 17:30:07 2013 -0400
@@ -0,0 +1,49 @@
+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)
+