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dev.ampliconrepository.org instructions

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Jens Luebeck edited this page Apr 5, 2024 · 4 revisions

For testing and prerelease purposes, we have a dev/beta test version of amplicon repository available at the url https://dev.ampliconrepository.org.

This runs inside a container on the same server as the production site to minimize costs. Because it requires AWS permissions to access the server, administration of the server is restricted to members of the UCSD "ucsd-cse-ampliconrepository-admin" group who all by default have access to the AWS console through UCSD SSO. This means that the intern developers may not update this server themselves.

Updating the dev server

  1. SSH into the server. The hostname and/or IP address is available in the AWS Console. You cannot ssh into "dev.ampliconrepository.org" as that is just the firewall/load balancer.

  2. cd ~/AmpliconRepository-dev.

  3. This is a clone of the AmpliconRepository git repo. git pull to get the latest code. Specify a branch if desired. At the time of this writing it is using the main branch. Note that this repository has several files (e.g. certificates, config) that are not part of the git repo, so please do not delete and re-clone it without caching these files and replacing them after the clone. Then do git checkout tags/[release]

  4. [If there are new environment vars/vars being changed, do the following steps] Stop the dev repository ./stop-server.sh

  5. Build the dev docker container. docker build -t genepattern/amplicon-repo:dev .

  6. If you used a different tag for your docker container, update "~/start-server.sh" to match the docker tag you wish to use.

  7. Start the server in the new container ./start-server.sh

  • If you run into the error: Error response from daemon: Conflict. The container name "/amplicon-dev" is already in use by container *container_id*. You have to remove (or rename) that container to be able to reuse that name., remove the Docker container using docker container rm *container_id*, and re-run ./start-server.sh.
  1. Verify the server is running, docker ps and look for container called amplicon-dev. Examine the logs in ~/AmpliconRepository-dev/logs. Point a browser at https://dev.ampliconrepository.org/ and verify it is running and using the correct version.
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