On Thu, Jan 15, 2015 at 6:57 PM, Ryan G <ngsbioinformat...@gmail.com> wrote:
> 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

The old pre-ToolShed way to add a new datatype was indeed to
add it to datatypes_conf.xml and put any Python file into the
galaxy-dist/lib/galaxy/datatypes/

I'm still doing this on some of my locally developed tools, but
now they are in the ToolShed perhaps I should switch to using
that...

Regards,

Peter

P.S. You also used to need to add an import line to the
galaxy-dist/lib/galaxy/datatypes/registry.py but that is not
longer required as of this bug fix:
https://bitbucket.org/galaxy/galaxy-central/commits/1422966f1ca88472b8685015f5a8cdd3dd0f1db9
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