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Mirror latest galaxy-lib changes for Conda and CWL improvements. #3742

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merged 1 commit into from Mar 17, 2017

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commented 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.

This is an expansion and redo of #3733.

@jmchilton jmchilton added this to the 17.05 milestone Mar 11, 2017

@jmchilton jmchilton force-pushed the jmchilton:galaxy-lib-20170311 branch 2 times, most recently from f0d446e to 7e6e2bd Mar 13, 2017

@jmchilton jmchilton added status/WIP and removed status/review labels Mar 13, 2017

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commented Mar 14, 2017

@galaxybot test this

Mirror latest galaxy-lib changes for Conda and CWL improvements.
- 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 jmchilton force-pushed the jmchilton:galaxy-lib-20170311 branch from 7e6e2bd to b1429d4 Mar 14, 2017

@jmchilton jmchilton added status/review and removed status/WIP labels Mar 15, 2017

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commented Mar 15, 2017

The circular import errors seem to have been resolved. Pulling this out of WIP.

@dannon dannon merged commit 031ce23 into galaxyproject:dev Mar 17, 2017

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