Unable to add R package dependency to tool_dependencies.xml

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Unable to add R package dependency to tool_dependencies.xml

bgrande
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 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 written by Björn and the <repository> tag description

Best regards, 
Bruno


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tool_dependencies.xml (1K) Download Attachment
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Re: Unable to add R package dependency to tool_dependencies.xml

Björn Grüning-3
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
> ​
>
>
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
>
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Re: Unable to add R package dependency to tool_dependencies.xml

Ross-2
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 <[hidden email]> 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
> ​
>
>
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
>
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/


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Re: Unable to add R package dependency to tool_dependencies.xml

Peter Cock
On Sat, Nov 1, 2014 at 2:30 AM, Ross <[hidden email]> wrote:

> 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 tool sheds.

Yes, I make heavy use of the default tool-shed attribute so that I can
upload the same XML file to either the Test Tool Shed or the main
Tool Shed. The only catch is making sure all the dependencies are
in both.

Peter

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