[galaxy-dev] Unable to add R package dependency to tool_dependencies.xml
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 ?xml version=1.0? tool_dependency package name=R_3_1_1 version=3.1.1 repository name=package_r_3_1_1 owner=fubar toolshed=http://testtoolshed.g2.bx.psu.edu/; / /package package name=exomecnv version=1.4 install version=1.0 actions_group action type=setup_r_environment repository name=package_r_3_1_1 owner=fubar toolshed=http://testtoolshed.g2.bx.psu.edu/; package name=R_3_1_1 version=3.1.1 / /repository /action /actions_group /install readme This installer downloads and installs ExomeCNV and its dependencies. /readme /package /tool_dependency ___ 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/
Re: [galaxy-dev] Unable to add R package dependency to tool_dependencies.xml
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/
Re: [galaxy-dev] Unable to add R package dependency to tool_dependencies.xml
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 ___ 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/ ___ 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/
