PegasusHub

A Community-enabled Workflows Repository for Pegasus

Adding your own workflow repository

In order to add your own Pegasus-enabled workflow repository, you only need to add your organization and repository names to the _data/workflows.yml file as follows:

- organization: my-github-organization
  repo_name: my-workflow-repository
  highlight: true
  priority: 2

The property highlight specifies wether the workflow is to be featured on the homepage. If highlight is set to true, the workflow must be given a priority number between 1 to 5 (5 being the most important and to be featured on top).

The Hub only pulls in information from the master branch of a workflows repository. More details about how to add more information describing your repository by specifying a .pegasushub.yml can be found at here.

The preferred way to submit your changes is via creating a pull request with the changes.

Starting your local instance of the Workflows Repository

The repository gets deployed automatically at https://pegasushub.io every 2 hours.

The website is a Ruby Jekyll site and you can run an instance of it locally on your desktop by doing the following

Generate the html pages

Before running the script, you need to set specify GitHub access token that allows the process.py script to retrieve information from the various GitHub repositories. This is done by setting the environment variable PEGASUSHUB_TOKEN

$ export PEGASUSHUB_TOKEN=xxxxxx

$ pip3 install -r requirements.txt
$ ./scripts/process.py
404 Client Error: Not Found for url: https://raw.githubusercontent.com/pegasus-isi/sra-search-pegasus-workflow/master/.pegasushub.yml
404 Client Error: Not Found for url: https://raw.githubusercontent.com/pegasus-isi/freesurfer-osg-workflow/master/.pegasushub.yml
404 Client Error: Not Found for url: https://raw.githubusercontent.com/pegasus-isi/mask-detection-workflow/master/.pegasushub.yml
404 Client Error: Not Found for url: https://raw.githubusercontent.com/pegasus-isi/molecular-transformer-workflow/master/.pegasushub.yml

The workflow html pages get generated in the _workflows directory and the _logs directory will have logs from the process script

Start the Jekyll Server

$ bundle install
$ bundle exec jekyll serve --incremental
Configuration file: /Volumes/lfs1/devel/Pegasus/git/pegasushub.github.io/_config.yml
            Source: /Volumes/lfs1/devel/Pegasus/git/pegasushub.github.io
       Destination: /Volumes/lfs1/devel/Pegasus/git/pegasushub.github.io/_site
 Incremental build: enabled
      Generating...
       Jekyll Feed: Generating feed for posts
                    done in 0.58 seconds.
 Auto-regeneration: enabled for '/Volumes/lfs1/devel/Pegasus/git/pegasushub.github.io'
    Server address: http://127.0.0.1:4000
  Server running... press ctrl-c to stop.