# HG changeset patch # User jorrit # Date 1360372334 18000 # Node ID 4f8ea94020b1b5d36cdc184352972ec0b7e75570 Uploaded diff -r 000000000000 -r 4f8ea94020b1 README --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README Fri Feb 08 20:12:14 2013 -0500 @@ -0,0 +1,11 @@ +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 diff -r 000000000000 -r 4f8ea94020b1 fetch_ontology.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fetch_ontology.xml Fri Feb 08 20:12:14 2013 -0500 @@ -0,0 +1,41 @@ + + from OBO repository + + obo-scripts + + obo-fetch-remote-ontology.pl $ont > $output + + + + + + + + + + + + + + + +.. class:: infomark + +Fetch entire ontology in OBO format + +**Example** + +Here are some common ID spaces:: + + GO gene ontology + CL cell ontology + +**More information** + +http://github.com/cmungall/obo-scripts + + + + + + diff -r 000000000000 -r 4f8ea94020b1 test-data/fetch_GO_ontology.test diff -r 000000000000 -r 4f8ea94020b1 test-data/output.eco.obo.contains --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output.eco.obo.contains Fri Feb 08 20:12:14 2013 -0500 @@ -0,0 +1,1 @@ +id: ECO:0000000 diff -r 000000000000 -r 4f8ea94020b1 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Fri Feb 08 20:12:14 2013 -0500 @@ -0,0 +1,20 @@ + + + + + + git clone http://github.com/cmungall/obo-scripts + + ./ + $INSTALL_DIR + + + $INSTALL_DIR + + + + + obo_scripts require perl to be installed. + + +