changeset 0:ad3d1d8ca3cc draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Thu Jan 08 12:43:34 2015 -0500
@@ -0,0 +1,33 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="perl_xml_simple" version="2.20">
+        <repository changeset_revision="2ba4c9419ceb" name="package_perl_xml_simple_2_20" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="bioperl" version="1.6.922">
+        <repository changeset_revision="bd1fcedd9aad" name="package_bioperl_1_6" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="prokka" version="1.10">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://www.vicbioinformatics.com/prokka-1.10.tar.gz</action>
+                <action type="shell_command">bin/prokka --setupdb</action>
+                <action type="move_directory_files">
+                    <source_directory>.</source_directory>
+                    <destination_directory>$INSTALL_DIR</destination_directory>
+                </action>
+                <action type="set_environment">
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions>
+        </install>
+    <readme>
+        Prokka is a software tool for the rapid annotation of prokaryotic genomes. A typical 4 Mbp genome can be 
+        fully annotated in less than 10 minutes on a quad-core computer, and scales well to 32 core SMP systems. 
+        It produces GFF3, GBK and SQN files that are ready for editing in Sequin and ultimately submitted to Genbank/DDJB/ENA.
+
+        http://www.vicbioinformatics.com/software.prokka.shtml
+
+        Warning: Prokka includes custom databases and is thus about a 340 MB download!
+    </readme>
+  </package>
+</tool_dependency>