I am skeptical that setting up a local tool shed is worth the effort -
it seems like overkill.  I think just downloading the tar balls,
manually modifying the datatypes_conf.xml is fine.

If you set the tool_dependencies_dir in your Galaxy configuration -
you can also create a isolated environments for tool requirements
(https://wiki.galaxyproject.org/Admin/Config/ToolDependencies)
allowing multiple versions of requirements like samtools to be
installed simultaneously. I recently added the ability to have
multiple versions of tools themselves installed like the tool shed but
without the tool shed
(https://bitbucket.org/galaxy/galaxy-central/commits/08f8850853d004bf8a456a147436a6694d0a1a11)
-  it is pretty experimental but it might help if you go down this
road.

As for how Galaxy knows about the tool shed installs - it is a
combination of file system files and database modifications (Galaxy
installs the dependencies into tool_dependencies_dir, the tool files
into the directory specified in shed_tools_conf.xml, updates the file
integrated_tool_panel_conf.xml, and registers tool lineages and
installation status in the Galaxy database). It should certainly be
possible to install tools from a different server than Galaxy is
running on - but you will need to run a Galaxy process on that server
that can access all the same files and the Galaxy database.

Hope this helps,

-John

On Fri, Jan 16, 2015 at 10:39 AM, Ryan G <ngsbioinformat...@gmail.com> wrote:
> 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.gruen...@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 <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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>> >
>
>
>
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