gladstone-institutes/MonkeyPipeline

MonkeyPipeline

Live version

Sean Thomas and Alex WIlliams 2013-2016
version 2 - parallelized for Rigel / works with TORQUE PBS scheudler (should work with other PBS schedulers). Can operate without a scheduler if you add "--notorque" to the command line.

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Basic Rules:

• Don't implement changes directly on the master branch.
• Implement fixes and features in a feature branch in your personal/local copy of the repo.
  • Push feature branches to a counterpart branch in remote/origin (i.e. GitHub) with the same name.
  • When done implementing fix or feature open a Pull Request (PR) to merge the changes into master.
  • Ideally have someone else review your code and approve those changes, i.e. approve the PR.
  • feature branch naming convention: initials-feature-branch-name, e.g. df-add_new_feature.
• Generally use git pull --rebase when pulling changes (say from master) from GitHub, and git merge when pushing changes up the hierarchy/GitHub. See these:
  • https://www.derekgourlay.com/blog/git-when-to-merge-vs-when-to-rebase/
  • https://www.atlassian.com/git/tutorials/merging-vs-rebasing
• TYPICAL ORDER OF STEPS (when you have local changes and you want to come up-to-date with remote): commit local changes, pull from remote, push to remote.

USAGE:

usage: monkey_agw -V [OPTIONS] <config_file.txt>