galaxy-pulsar-dev

Overview

A Docker Compose-based solution for easing the development and testing of Pulsar with Galaxy.

Most development setups are not going to find the sorts of bugs that commonly occur in production since in development, all paths are on the same host and accessible to both the Galaxy and Pulsar servers, which run as the same user. galaxy-pulsar-dev exists to develop and test your changes on a production-like setup, with RabbitMQ and privilege/host separation.

In addition, Galaxy and Pulsar are tightly coupled (Galaxy imports Pulsar libs, Pulsar imports Galaxy libs). This project makes it easy to run your changes to the Pulsar client library in Galaxy.

This project evolved from a single script created in preparation for the Galaxy Community Conference 2021 CoFest.

Usage

You must have Docker and Docker Compose installed.

To start, run:

$ make up

This does a bit of one-time preparation:

• Creating the Docker Compose .env file
• Cloning Galaxy and Pulsar at ../galaxy and ../pulsar, respectively
• Creating Galaxy's virtualenv at galaxy/venv and installing its dependencies
• Building Galaxy's client, if necessary

After which, it runs docker-compose up. As is normal with foreground Docker Compose sessions, hit Ctrl-C to terminate. To start daemonized, run:

$ make up-d

And to stop:

$ make down

Once the one-time setup has been performed, you can forego the Makefile and run docker-compose commands directly, if you prefer.

It is often ideal to leave PostgreSQL and RabbitMQ running while only restarting Galaxy and/or Pulsar, especially since no persistence is configured for PostgreSQL (intentionally). After starting (daemonized, or from another terminal), you can restart Galaxy and Pulsar with:

$ make restart

Or you can restart individual services like so:

$ docker-compose restart galaxy-web galaxy-job  # restart Galaxy
$ docker-compose restart pulsar                 # restart Pulsar

To reset to the initial state, run:

$ make clean

This removes .env, the virtualenvs, and Galaxy and Pulsar state directories, but not the Galaxy and Pulsar clones (even if it created them). It also removes the Docker containers and images.

pulsar-galaxy-lib

Pulsar's client library is installed in Galaxy at a pinned version from the packages on PyPI, but it is often desirable when developing to install the Pulsar client library from your development clone of Pulsar instead. This can be acheived by running:

$ make pulsar-galaxy-lib
$ docker-compose restart galaxy-web galaxy-job

The single script version of this project attempted to do this step for you automatically as-needed, but that's a bit harder to do in the Compose setup, so you have to trigger it manually for now.

Customization

To use Galaxy and/or Pulsar clones at different (perhaps preexisting) paths, generate .env first with:

$ make .env

Then edit .env and set $GALAXY_ROOT and/or $PULSAR_ROOT accordingly.

Additional Notes

The directory galaxy/config/ is mounted into the container over Galaxy's config directory, so you can make changes to Galaxy's config there as needed.

Galaxy and Pulsar's virtualenvs and state directories are maintained outside of their respective clones and bind mounted in, so using this should not interfere with your normal virtualenvs, job directories, etc. in those clones. The Galaxy client is built and installed to the static/ directory of the clone, however.

These Galaxy users may be useful (you need to register them yourself):

• [email protected]: Galaxy Admin
• [email protected]: Runs all jobs locally
• [email protected]: Runs all jobs (except upload1) via Pulsar

To query the database, you can use:

$ docker-compose exec postgres psql -U galaxy -w galaxy

Currently, Galaxy and Pulsar maintain their own Conda installs, for isolation and more realistic testing. You may find this slow, space-consuming, and annoying if you're testing a lot of tools. If so, you can mount Galaxy's conda into Pulsar's venv in docker-compose.yml and adjust pulsar/config/app.yml accordingly.