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another try at adding amigo tool
author Seth Carbon <sjcarbon@lbl.gov>
date Fri, 29 Mar 2013 14:17:34 -0700
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1 Welcome to OBO Tool Repository for BBOP Galaxy
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Seth Carbon <sjcarbon@lbl.gov>
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3 The following libraries need to be installed to use the obo tools:
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5 # termfinder needs g++ and other build tools
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6 sudo apt-get $APT_OPTS install build-essential
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8 # perl dbi / perl DBD::mysql
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9 sudo apt-get $APT_OPTS install libdbi-perl libdbd-mysql-perl
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11 # GO:TermFinder needs dependencies GraphViz and GD graphics libraries
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12 sudo apt-get $APT_OPTS install libgraphviz-perl
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13 sudo apt-get $APT_OPTS install libgd-gd2-perl
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15 # subversion for retrieving versioned gene ontologies
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16 sudo apt-get $APT_OPTS install subversion
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17
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18 --- Term Enrichment related ---
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19 (currently used - heavily tied to mysql / old data model)
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20 http://geneontology.svn.sourceforge.net/viewvc/geneontology/go-dev/trunk/amigo/amigo/cgi-bin/term_enrichment?view=log
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22 (command line version - file based)
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23 http://geneontology.svn.sourceforge.net/viewvc/geneontology/go-dev/trunk/go-db-perl/
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25 http://geneontology.svn.sourceforge.net/viewvc/geneontology/go-dev/trunk/go-db-perl/scripts/go-find-enriched-terms.pl?view=log
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27 --- Gene Associations ---
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28 svn --ignore-externals co svn://ext.geneontology.org/trunk/gene-associations gene-associations
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30 --- AmiGO related ---
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32 for AmiGO Manual
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33 http://wiki.geneontology.org/index.php/AmiGO_Manual:_Visualize
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34
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35 online tool to play around (current version, has R Wrapper ramigo)
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36 http://amigo.geneontology.org/cgi-bin/amigo/visualize?mode=client
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37
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38 online tool Amigo2
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39 http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo?mode=visualize
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41 entry point Amigo2
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42 https://github.com/kltm/amigo/blob/master/perl/bin/visualize
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44 --- workflows ---
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46 gene set + ontology + gene associations =
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48 gene products + background set = (good) + (ambiguous) + (no match, missing)
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