# 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
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+The following libraries need to be installed to use the obo tools:
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+# termfinder needs g++ and other build tools
+sudo apt-get $APT_OPTS install build-essential
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+# perl dbi / perl DBD::mysql
+sudo apt-get $APT_OPTS install libdbi-perl libdbd-mysql-perl
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+# 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
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+ from OBO repository
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+ obo-scripts
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+ obo-fetch-remote-ontology.pl $ont > $output
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+.. class:: infomark
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+Fetch entire ontology in OBO format
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+**Example**
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+Here are some common ID spaces::
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+ GO gene ontology
+ CL cell ontology
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+**More information**
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+http://github.com/cmungall/obo-scripts
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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
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+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
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+ git clone http://github.com/cmungall/obo-scripts
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+ ./
+ $INSTALL_DIR
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+ $INSTALL_DIR
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+ obo_scripts require perl to be installed.
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