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Allow extra volume bindings and custom wrapper config file #678

Merged
merged 4 commits into from
Sep 4, 2022

Commits on Aug 30, 2022

  1. Add ODK_BINDS option to run.sh.

    Add a new overridable variable to the `run.sh` script to allow users to
    specify extra volume bindings. If set, the variable should contain a
    comma-separated list of bindings of the form:
    
      <directory on the host>:<mounting point in the container>[:options]`
    gouttegd committed Aug 30, 2022
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Commits on Aug 31, 2022

  1. Add ODK_DOCKER_OPTIONS variable to the run.sh script.

    Allow users to pass arbitrary options to the `docker run` command by
    setting the `ODK_DOCKER_OPTIONS` variable prior to calling the `run.sh`
    script.
    
    Likewise, users of Singularity can set the `ODK_SINGULARITY_OPTIONS`
    variable to pass arbitrary options to the `singularity exec` command.
    gouttegd committed Aug 31, 2022
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  2. Source a run.sh.conf file if it exists.

    Make the `run.sh` wrapper script check for a `run.sh.conf` file in the
    `src/ontology` directory, and source that file if it exists.
    
    This is to allow users to customize the behaviour of the wrapper script
    by setting any of the ODK_* variable in that `run.sh.conf` file, instead
    of having to export them in the environment or to manually set them at
    each invocation of the wrapper script.
    
    The `run.sh.conf` file is excluded from version control. It is intended
    for local use only, not to be shared between all editors of the
    ontology.
    gouttegd committed Aug 31, 2022
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  3. Update CHANGELOG.md.

    gouttegd committed Aug 31, 2022
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