Hi, Bruno.
As Björn points out, cross-toolshed dependencies aren't currently supported
but exporting (eg) package_r_3_1_1 as a capsule (make sure to include ALL
dependencies) from one toolshed and importing that capsule into your own
local toolshed brings all the sub-dependent packages so they exist locally.
One trick: if the toolshed URL is NOT specified in a package reference in
tool_dependencies.xml, the local toolshed will be sourced as the default.
Not sure if this makes much sense, but it works for me developing on my
laptop's toolshed with lots of packages that came through capsules from the
main and other toolsheds.
On Sat, Nov 1, 2014 at 10:49 AM, Björn Grüning <bjoern.gruen...@gmail.com>
wrote:

> Hi Bruno,
>
> it is currently not possible to specify dependencies from other Tool
> Sheds. So you can only depend on packages that are in the same Tool Shed
> as your tool.
>
> Is this your main issue?
>
> Greg has some nice blog posts about the Tool Shed and how to set up a
> local test Tool Shed with other packages, like the one from foobar.
>
> http://gregvonkuster.org/
>
> Cheers,
> Bjoern
>
>
> > 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
> > ​
> >
> >
> >
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