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