Fix various issues with installation of CamCHILDMine

[martinburchell]

In the process of getting the 2022 FAIR TREATMENT (CamCHILDMine) demo working I ended up making these changes. In summary:

• New GitHub workflow for building the docker images with the default Biotestmine
• Remove obsolete version from docker compose YAML files
• Abort build.sh if any part of the script fails unexpectedly
• Store docker-compose defaults in .env file
• Reduce some complexity in build.sh when resolving environment variables
• Use wait-for-it to ensure the various containers are running (bundled in as there is no Alpine package)
• Do not try to copy malaria-data.tar.gz if it is not present
• Remove the duplicate call to gradlew cargoDeployRemote. In CamCHILDMine I've implemented the workaround described in Gradle needs to start or deploy a second time to serve webapp intermine#2162 (comment)
• Use named volumes in the local.docker-compose.yml. I've removed the parsing of the YAML file in mkdatadirs.sh as this seemed like a brittle approach and made this script runnable from anywhere.
• Sort out various permissions issues.

There was a bit of guesswork involved so I'd appreciate another set of eyes on this.

[leoank]

Overall it look good to me.

[leoank]

@heralden please have a look as well. This PR introduces some ARGS expected by the intermine_builder dockerfile. Is this going to break any of our existing pipelines?

[heralden]

@martinburchell

Remove the duplicate call to gradlew cargoDeployRemote. In CamCHILDMine I've implemented the workaround described in intermine/intermine#2162 (comment)

In case it may be of use, we found another workaround for this issue is to ensure the war task is run first.

./gradlew war --stacktrace
./gradlew cargoDeployRemote --stacktrace
./gradlew cargoRedeployRemote --stacktrace 

[heralden]

Apologies for the very late review.

This project is only used as a git submodule in https://github.com/intermine/intermine_boot and neither are depended on for active deployments of intermine. Hence it should be safe to make drastic changes to this repo and various improvements. Please go ahead and merge this, and if you want to make further improvements, I'm fine with those getting merged as well without my review.