changeset 0:4f8ea94020b1

Uploaded

--- /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

--- /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 @@
+<tool id="fetch-remote-ontology" name="fetch remote ontology" version="0.0.13">
+  <description>from OBO repository</description>
+  <requirements>
+    <requirement type="package" version="1.0.11">obo-scripts</requirement>
+  </requirements>
+  <command>obo-fetch-remote-ontology.pl $ont > $output</command>
+  <inputs>
+    <param name="ont" type="text" size="50" value="" label="Ontology ID Space" />
+  </inputs>
+  <outputs>
+    <data format="obo" name="output" />
+  </outputs>
+  <tests>
+    <test>
+     <param name="ont" value="ECO" />
+     <output name="output" file="output.eco.obo.contains" compare="contains"/>
+    </test>
+  </tests>
+
+
+  <help>
+.. 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
+
+  </help>
+
+</tool>
+
+

--- /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

--- /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 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="obo-scripts" version="1.0.11">
+        <install version="1.0">
+            <actions>
+                <action type="shell_command">git clone http://github.com/cmungall/obo-scripts</action>
+		<action type="move_directory_files">
+                    <source_directory>./</source_directory>
+                    <destination_directory>$INSTALL_DIR</destination_directory>
+                </action>
+		<action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+		obo_scripts require perl to be installed.
+        </readme>
+    </package>
+</tool_dependency>