obotools_02: README annotate

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Try at a fresh start...

author	kltm
date	Fri, 29 Mar 2013 17:30:07 -0400
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rev	line source
0 028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	1 Welcome to OBO Tool Repository for BBOP Galaxy
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	2
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	3 The following libraries need to be installed to use the obo tools:
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	4
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	5 # termfinder needs g++ and other build tools
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	6 sudo apt-get $APT_OPTS install build-essential
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	7
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	8 # perl dbi / perl DBD::mysql
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	9 sudo apt-get $APT_OPTS install libdbi-perl libdbd-mysql-perl
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	10
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	11 # GO:TermFinder needs dependencies GraphViz and GD graphics libraries
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	12 sudo apt-get $APT_OPTS install libgraphviz-perl
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	13 sudo apt-get $APT_OPTS install libgd-gd2-perl
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	14
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	15 # subversion for retrieving versioned gene ontologies
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	16 sudo apt-get $APT_OPTS install subversion
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	17
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	18 --- Term Enrichment related ---
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	19 (currently used - heavily tied to mysql / old data model)
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	20 http://geneontology.svn.sourceforge.net/viewvc/geneontology/go-dev/trunk/amigo/amigo/cgi-bin/term_enrichment?view=log
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	21
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	22 (command line version - file based)
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	23 http://geneontology.svn.sourceforge.net/viewvc/geneontology/go-dev/trunk/go-db-perl/
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	24
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	25 http://geneontology.svn.sourceforge.net/viewvc/geneontology/go-dev/trunk/go-db-perl/scripts/go-find-enriched-terms.pl?view=log
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	26
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	27 --- Gene Associations ---
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	28 svn --ignore-externals co svn://ext.geneontology.org/trunk/gene-associations gene-associations
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	29
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	30 --- AmiGO related ---
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	31
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	32 for AmiGO Manual
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	33 http://wiki.geneontology.org/index.php/AmiGO_Manual:_Visualize
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	34
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	35 online tool to play around (current version, has R Wrapper ramigo)
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	36 http://amigo.geneontology.org/cgi-bin/amigo/visualize?mode=client
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	37
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	38 online tool Amigo2
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	39 http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo?mode=visualize
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	40
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	41 entry point Amigo2
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	42 https://github.com/kltm/amigo/blob/master/perl/bin/visualize
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	43
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	44 --- workflows ---
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	45
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	46 gene set + ontology + gene associations =
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	47
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	48 gene products + background set = (good) + (ambiguous) + (no match, missing)
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	49

Mercurial > repos > kltm > obotools_02

annotate README @ 0:028babd7a6c5 draft default tip