Allow extra volume bindings and custom wrapper config file #678
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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]`
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.
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.
matentzn
reviewed
Sep 1, 2022
matentzn
approved these changes
Sep 2, 2022
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This PR:
a) Adds a new
ODK_BINDSvariable to therun.shwrapper script, which can be used to specify extra volume bindings within the Docker or Singularity container. Use as follows:b) Adds a new
ODK_DOCKER_OPTIONSvariable, to allow user to pass any custom options to the invocation ofdocker run. Another variable,ODK_SINGULARITY_OPTIONS, does the same for the invocation ofsingularity exec.c) Allows to set variables for the
run.shwrapper in a file namedrun.sh.conf(in the same directory as the wrapper script itself). That file should contain standard Bourne-shell variable declarations, and will be sourced (if it exists) by the wrapper script. It allows to use variables such as the newODK_BINDS,ODK_DOCKER_OPTIONS, but also the pre-existingODK_IMAGEorODK_TAG, once and for all in therun.sh.conffile, instead of having to export them to the user’s environment or set them every time the wrapper script is invoked.closes #675