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Allow conda to be configured to use locally built packages.#47
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jmchilton merged 1 commit intogalaxyproject:masterfrom Feb 24, 2017
Merged
Allow conda to be configured to use locally built packages.#47jmchilton merged 1 commit intogalaxyproject:masterfrom
jmchilton merged 1 commit intogalaxyproject:masterfrom
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This is required to run tests and such with new and updated local packages before they have been published.
nsoranzo
reviewed
Feb 24, 2017
| shell_exec=None, debug=False, ensure_channels='', | ||
| condarc_override=None, use_path_exec=USE_PATH_EXEC_DEFAULT, copy_dependencies=False): | ||
| condarc_override=None, use_path_exec=USE_PATH_EXEC_DEFAULT, | ||
| use_local=USE_LOCAL_DEFAULT, copy_dependencies=False): |
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I think I'd add use_local as last parameter (at least for consistency with how you call it in galaxy/tools/deps/resolvers/conda.py)
bgruening
approved these changes
Feb 24, 2017
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Awesome - thanks for the reviews all. I made the change requested in master @nsoranzo. |
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Test case for this PR included in galaxyproject/planemo#643. |
jmchilton
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Mar 9, 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. - 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. 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 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
added a commit
to jmchilton/galaxy
that referenced
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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
added a commit
to jmchilton/galaxy
that referenced
this pull request
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
added a commit
to jmchilton/galaxy
that referenced
this pull request
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
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This is required to run tests and such with new and updated local packages before they have been published.