I'm attempting to create a tool dependency definition file for ExomeCNV,
which notably depends on R (I'm trying to use the package_r_3_1_1
repository). However, I can't seem to set up the dependency properly. See
attached for my tool_dependencies.xml. Also, see here <http://cl.ly/YK3C>
for the error message when I attempt to upload the tool_dependencies.xml
file to the Tool Shed.
One of the possible issues is that the toolshed repository tag attribute
for specifying an external Tool Shed isn't being considered. This is being
done in a local Tool Shed installation that doesn't include
the package_r_3_1_1 repository. Therefore, I must refer to the Test Tool
Shed. This is inspired by a tool definition
<https://github.com/bgruening/galaxytools/blob/78f35bc97160bdfe4783c9ac2e017e9fe55e041c/packages/package_deseq2_1_0_17/tool_dependencies.xml>
written by Björn and the <repository> tag description
<https://wiki.galaxyproject.org/ToolDependenciesTagSets>.
Best regards,
Bruno
<?xml version="1.0"?>
<tool_dependency>
<package name="R_3_1_1" version="3.1.1" >
<repository name="package_r_3_1_1" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu/"; />
</package>
<package name="exomecnv" version="1.4">
<install version="1.0">
<actions_group>
<action type="setup_r_environment">
<repository name="package_r_3_1_1" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu/";>
<package name="R_3_1_1" version="3.1.1" />
</repository>
</action>
</actions_group>
</install>
<readme>
This installer downloads and installs ExomeCNV and its dependencies.
</readme>
</package>
</tool_dependency>
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