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
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.
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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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.gruening@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.
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/78f35bc97160bdfe4783c9ac2e017e...
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/
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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/
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On Sat, Nov 1, 2014 at 2:30 AM, Ross ross.lazarus@gmail.com 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
galaxy-dev@lists.galaxyproject.org
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Björn Grüning -
Bruno Grande -
Peter Cock -
Ross