Updated the docker-compose.yml so that it acts as a back-up file. Parameterised more of docker-compose.yml for portability.
Installed nano and jq in the web container, for easier troubleshooting.
closes #74
closes #71
Test set-up
Edited the docker-compose.yml, config file, and env file in the development environment, to match the same format as in GitHub
Set up a .env file on my local laptop and used 'docker compose build' to make test images, which should incorporate jq and nano into the genetics-ark-web container. Retagged the new images to 'update_compose'.
Saved the test web image as a file, file-GkjZF1Q4J91vyF72xg08JXvK, copied it to the development environment, and loaded the image from the file.
Edited the development 'docker-compose.yml' to use the test-tagged versions of 'genetics-ark-web:update_compose' and 'genetics-ark-cron:issue_70', instead of the last release, 2.0.3
Ran the docker-compose.yml to start Genetics Ark
Exec'd into the cron job container to run the updater automatically
Test results
When exec'd into the web container, jq gives help information, and nano opens an editor with 'Welcome to nano', rather than throwing errors about the tools not being found
Genetics Ark front page shows on dev without nginx errors
The Service Desk link-out works
Primer Designer:
Produces an output PDF with a straightforward example
Reference files, primer version, e.t.c (annotated from config) in the metadata section at the bottom of the PDF look normal
IGV:
Logs in normally
Sample search for '101' returns a list of results
Able to open and view IGV in browser for a recent sample
Updated the docker-compose.yml so that it acts as a back-up file. Parameterised more of docker-compose.yml for portability. Installed nano and jq in the web container, for easier troubleshooting. closes #74 closes #71
Test set-up
Test results
This change is