I can try a local toolshed, but the organization I work at frowns upon automatic installation for various reasons. That and it lets me see exactly how a tool is installed and works within my local instance.

When a tool is installed from the toolshed, how does Galaxy know about it? From a DB entry, or from the XML file(s) being present somewhere? I sort of like the idea of how /etc/profile.d gets scanned by /etc/bashrc when a user logs into a linux machine. This way, there is no modification of files, just placing the right files in the right directory is all that is needed. Anyway, I need to understand how Galaxy works with the toolshed.

On Fri, Jan 16, 2015 at 3:08 AM, Björn Grüning <bjoern.gruening@gmail.com> wrote:

Hi Ryan,

what about a local bootstrapped ToolShed which is in sync with the
public one (at least for the users you are interested on). Than you can
install from this ToolShed. I guess this is less annoying than
maintaining everything on your own.

Cheers,
Bjoern

Am 16.01.2015 um 08:22 schrieb Peter Cock:

> On Thu, Jan 15, 2015 at 6:57 PM, Ryan G <ngsbioinformatics@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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