Because of the way the infrastructure for my Galaxy instance is set up, I
need to download and install tools from the toolshed manually.  For most of
the tools, this is pretty easy, however I'm now trying to add RSEM to my
instance and it has some new datatypes.

Along with the new data types is python class file.  I'm referring to the
exist datatypes_conf.xml.sample but don't see a reference to datatype_files
as is coded in the RSEM tool.

So my question is, how can I manually install a tool such as RSEM from the
toolshed?  I've cloned it but not sure where to put the files and what to
modify in Galaxy's configuration to see the new files.  I can modify the
datatypes_conf.xml and include the datatypes, but I get the sense this is
not correct.

Ryan
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