This project is a Python server application that allows a Galaxy server to run jobs on remote systems (including Windows) without requiring a shared mounted file systems. Unlike traditional Galaxy job runners - input files, scripts, and config files may be transferred to the remote system, the job is executed, and the results are transfered back to the Galaxy server - eliminating the need for a shared file system.
Full documentation for the project can be found on Read The Docs.
Galaxy job runners are configured in Galaxy’s
job_conf.xml file. Some small
examples of how to configure this can be found here, but be sure
to check out
job_conf.xml.sample_advanced in your Galaxy code base or on
for complete information.
Full details on different ways to install Pulsar can be found in the install section of the documentaiton, but if your machine has the proper Python dependencies available it can be quickly download and a test job run with:
$ mkdir pulsar $ cd pulsar $ python3 -m venv venv $ . venv/bin/activate # venv\Scripts\activate.bat on Windows $ pip install 'pulsar-app[web]' $ pulsar-config $ pulsar --daemon # just `pulsar` on Windows $ pulsar-check # runs a test job
Please note that as of the 0.14.0 release, Pulsar no longer supports any version of Python 2. The minimum supported Python version is 3.5.
The configuration documentation has many details on securing your Pulsar server and enabling advanced features such as cluster integration and message queue communication.
Development and Testing¶
The recommended approach to setting up a development environment for Pulsar on Linux or macOS is rougly as follows:
$ git clone https://github.com/galaxyproject/pulsar $ cd pulsar $ python3 -m venv .venv $ . .venv/bin/activate # .venv\Scripts\activate on Windows $ pip install -e '.[web]' $ pip install -r dev-requirements.txt
-e flag to
pip installs Pulsar in “editable” mode, meaning that
changes you make to the source code will be reflected when running the pulsar
commands installed in the virtual environment.
This project is distributed with unit and integration tests (many of which will not run under Windows), the following command will install the needed python components to run these tests. The following command will then run these tests:
$ make tests
The following command will then produce a coverage report corresponding to this
test and place it in the
coverage_html_report subdirectory of this
$ coverage html
Check out the Contributing documentation for many more details on developing and contributing to Pulsar.
Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.
This documentation is an incomplete work in progress. There are more ways to configure and use Pulsar than are documented, and a growing number of Pulsar experts who would be more than happy to answer your questions and help with any problems you may run in to while setting up a Pulsar deployment. Please do not hesitate to reach out on the Galaxy Admins Gitter Channel