improved doc in galaxy.ini for outputs_to_working_directory #5332
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to avoid misconfigurations as in galaxyproject#5323
mvdbeek
reviewed
Jan 18, 2018
config/galaxy.ini.sample
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| # This option will override tool output paths to write outputs to the working | ||
| # directory (instead of to the file_path) and the job manager will move the | ||
| # outputs to their proper place in the dataset directory on the Galaxy server | ||
| # after the job completes. This is necessary (for example) you run on a cluster |
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s/is necessary (for example) you/is necessary (for example) if jobs/
config/galaxy.ini.sample
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| # outputs to their proper place in the dataset directory on the Galaxy server | ||
| # after the job completes. This is necessary (for example) you run on a cluster | ||
| # and your datasets (file_path) can not be written by the user running the jobs | ||
| # (e.g. if the filesystem is mounted read-only or the jobs are run by a |
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There's a a extra whitespace here.
config/galaxy.ini.sample
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| # directory (instead of to the file_path) and the job manager will move the | ||
| # outputs to their proper place in the dataset directory on the Galaxy server | ||
| # after the job completes. This is necessary (for example) you run on a cluster | ||
| # and your datasets (file_path) can not be written by the user running the jobs |
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s/and your datasets (file_path) can not be written/and datasets are not writable/
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I'd say: "and the output datasets cannot be created inside file_path by the user running the jobs"
to avoid misconfigurations as in galaxyproject#5323
…ub.com/bernt-matthias/galaxy into topic/outputs_to_working_directory-doc
nsoranzo
reviewed
Jan 18, 2018
config/galaxy.ini.sample
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| # paths to write outputs to the working directory instead, and the job manager | ||
| # will move the outputs to their proper place in the dataset directory on the | ||
| # Galaxy server after the job completes. | ||
| # This option will override tool output paths to write outputs to the working |
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s/the working/the job working/
nsoranzo
reviewed
Jan 18, 2018
config/galaxy.ini.sample
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| @@ -1333,7 +1335,7 @@ use_interactive = True | |||
| # actual user instead of as the user running the Galaxy server process. For | |||
| # details on these options, see the documentation at: | |||
| # | |||
| # https://galaxyproject.org/admin/config/performance/cluster | |||
| # https://galaxyproject.org/admin/config/performance/cluster#configuration | |||
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nsoranzo
reviewed
Jan 18, 2018
config/galaxy.ini.sample
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| @@ -1333,7 +1335,7 @@ use_interactive = True | |||
| # actual user instead of as the user running the Galaxy server process. For | |||
| # details on these options, see the documentation at: | |||
| # | |||
| # https://galaxyproject.org/admin/config/performance/cluster | |||
| # https://galaxyproject.org/admin/config/performance/cluster#submitting-jobs-as-the-real-user | |||
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Because of the redirect the anchor will not work, please use: https://docs.galaxyproject.org/en/latest/admin/cluster.html#submitting-jobs-as-the-real-user
nsoranzo
approved these changes
Jan 19, 2018
|
galaxy.ini.sample is gone - I ported these changes to new config in the PR linked above, thanks @bernt-matthias ! |
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to avoid misconfigurations as in #5323
furthermore I reordered the description such that first the option is described and then the use case