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Create default data directories in Dockerfile

Tor Solli-Nowlan requested to merge add-data-dirs-to-dockerfile into dev

Description

Several directories will be mounted from the host OS in production use, but there are no default locations set. Here we set and then create these default paths so that Docker doesn't "helpfully" create them as root owned. The relevant env variables are also set with these paths, but may/should be overridden with different values in dev/testing environments.

Related issues

Notes to review (code/docs/QA)

Setting ATTACHMENT_STORAGE, ANALYSES_INCOMING, ANALYSES_PATH, IGV_DATA in the base Docker layer may have some unexpected downstream impact as we currently set those variables in several different places. We really shouldn't be doing that anyway, so all the better if this helps us unify where/how we define things.

Tests

General

  • Tests have been added that prove my fix is effective or that my feature works
  • Related tests have been modified/removed

Hypothesis testing:

  • Soak testing has been done
  • Distribution between positive / negative cases has been checked

Database

  • Includes changes to database schema
  • Includes necessary database migrations

Configuration

  • Includes changes to configuration
  • Includes configuration migration instructions in documentation

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