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>
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/