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Add location fetching for Galaxy tools.#52
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jmchilton merged 1 commit intogalaxyproject:masterfrom Mar 10, 2017
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Depends on galaxy-lib enhancements from galaxyproject/galaxy-lib#52.
This allows Planemo to do some cool stuff like running CWL tools right from dockstore: planemo run dockstore://quay.io/briandoconnor/dockstore-tool-md5sum job.json But would also be useful for linting tools and such from URLs.
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jmchilton
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Mar 10, 2017
Depends on galaxy-lib enhancements from galaxyproject/galaxy-lib#52.
jmchilton
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Mar 10, 2017
Depends on galaxy-lib enhancements from galaxyproject/galaxy-lib#52.
jmchilton
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Mar 11, 2017
- I added more flexibility to mulled operations to work around bugs on OS X (galaxyproject/galaxy-lib#50). - I added the ability to use local packages with the Conda resolver (galaxyproject/galaxy-lib#47) - this allows Galaxy when used with Planemo to use locally built packages. Including Nicola's suggested changes here (galaxyproject/galaxy-lib@6d53fc7). - I switched the default Conda prefix to miniconda3 so the name matches what Galaxy is actually installing. galaxyproject/galaxy-lib#48. This would never actually be used with Galaxy since we decided it should maintain its own prefix rather than using the default - it is important for Planemo though. - I synced the galaxy.tools.cwl package with my latest downstream work that provides updates for latest developments in cwltool. galaxyproject/galaxy-lib#53 - I added the ability to load tools via URI-like strings in addition to simple paths - this allows referencing URLs and Dockstore/GA4GH tools directly from the command-line with Planemo. galaxyproject/galaxy-lib#52 There are some other bug fixes outside of these three main PRs related to the second point - minor refinements to get conda-build dependencies working and working automatically. - galaxyproject/galaxy-lib@bdacc4d - galaxyproject/galaxy-lib@1b7bca6 - galaxyproject/galaxy-lib@36b2e65
jmchilton
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Mar 13, 2017
- I added more flexibility to mulled operations to work around bugs on OS X (galaxyproject/galaxy-lib#50). - I added the ability to use local packages with the Conda resolver (galaxyproject/galaxy-lib#47) - this allows Galaxy when used with Planemo to use locally built packages. Including Nicola's suggested changes here (galaxyproject/galaxy-lib@6d53fc7). - I switched the default Conda prefix to miniconda3 so the name matches what Galaxy is actually installing. galaxyproject/galaxy-lib#48. This would never actually be used with Galaxy since we decided it should maintain its own prefix rather than using the default - it is important for Planemo though. - I synced the galaxy.tools.cwl package with my latest downstream work that provides updates for latest developments in cwltool. galaxyproject/galaxy-lib#53 - I added the ability to load tools via URI-like strings in addition to simple paths - this allows referencing URLs and Dockstore/GA4GH tools directly from the command-line with Planemo. galaxyproject/galaxy-lib#52 There are some other bug fixes outside of these three main PRs related to the second point - minor refinements to get conda-build dependencies working and working automatically. - galaxyproject/galaxy-lib@bdacc4d - galaxyproject/galaxy-lib@1b7bca6 - galaxyproject/galaxy-lib@36b2e65
jmchilton
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Mar 13, 2017
jmchilton
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Mar 13, 2017
- I added more flexibility to mulled operations to work around bugs on OS X (galaxyproject/galaxy-lib#50). - I added the ability to use local packages with the Conda resolver (galaxyproject/galaxy-lib#47) - this allows Galaxy when used with Planemo to use locally built packages. Including Nicola's suggested changes here (galaxyproject/galaxy-lib@6d53fc7). - I switched the default Conda prefix to miniconda3 so the name matches what Galaxy is actually installing. galaxyproject/galaxy-lib#48. This would never actually be used with Galaxy since we decided it should maintain its own prefix rather than using the default - it is important for Planemo though. - I synced the galaxy.tools.cwl package with my latest downstream work that provides updates for latest developments in cwltool. galaxyproject/galaxy-lib#53 - I added the ability to load tools via URI-like strings in addition to simple paths - this allows referencing URLs and Dockstore/GA4GH tools directly from the command-line with Planemo. galaxyproject/galaxy-lib#52 There are some other bug fixes outside of these three main PRs related to the second point - minor refinements to get conda-build dependencies working and working automatically. - galaxyproject/galaxy-lib@bdacc4d - galaxyproject/galaxy-lib@1b7bca6 - galaxyproject/galaxy-lib@36b2e65
jmchilton
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Mar 14, 2017
- I added more flexibility to mulled operations to work around bugs on OS X (galaxyproject/galaxy-lib#50). - I added the ability to use local packages with the Conda resolver (galaxyproject/galaxy-lib#47) - this allows Galaxy when used with Planemo to use locally built packages. Including Nicola's suggested changes here (galaxyproject/galaxy-lib@6d53fc7). - I switched the default Conda prefix to miniconda3 so the name matches what Galaxy is actually installing. galaxyproject/galaxy-lib#48. This would never actually be used with Galaxy since we decided it should maintain its own prefix rather than using the default - it is important for Planemo though. - I synced the galaxy.tools.cwl package with my latest downstream work that provides updates for latest developments in cwltool. galaxyproject/galaxy-lib#53 - I added the ability to load tools via URI-like strings in addition to simple paths - this allows referencing URLs and Dockstore/GA4GH tools directly from the command-line with Planemo. galaxyproject/galaxy-lib#52 There are some other bug fixes outside of these three main PRs related to the second point - minor refinements to get conda-build dependencies working and working automatically. - galaxyproject/galaxy-lib@bdacc4d - galaxyproject/galaxy-lib@1b7bca6 - galaxyproject/galaxy-lib@36b2e65
jmchilton
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Mar 15, 2017
Depends on galaxy-lib enhancements from galaxyproject/galaxy-lib#52.
jmchilton
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Mar 15, 2017
Depends on galaxy-lib enhancements from galaxyproject/galaxy-lib#52.
jmchilton
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Mar 15, 2017
Depends on galaxy-lib enhancements from galaxyproject/galaxy-lib#52.
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This allows Planemo to do some cool stuff like running CWL tools right from dockstore:
planemo run dockstore://quay.io/briandoconnor/dockstore-tool-md5sum job.json
But would also be useful for linting tools and such from URLs.