Sisyphus

A workflow manager in Python.

Installation

Requirements

Sisyphus requires a Python >=3.5 installation with the following additional libraries:

pip3 install -r requirements.txt

Optional if curse based user interface should be used:

pip3 install urwid

Optional if web interface should be used:

pip3 install flask

Optional to compile documentation:

pip3 install Sphinx

Optional if virtual file system should be used:

pip3 install fusepy
sudo addgroup $USER fuse  # depending on your system

Optional for a nicer traceback

pip3 install better_exchook

Setup

• Add sis to the PATH env, or symlink it, or call it directly.
• The current directory (pwd), when you run sis, should have a file settings.py (see example dir).
• Create a directory work in the current dir. All data created while running the jobs will be stored there.
• Create a directory output in the current dir. All the registered output will end up here.
• Create a directory alias in the current dir.
• Run sis --config some_config.py m.

Documentation

Can be found here: sisyphus-workflow-manager.readthedocs.io.

Example

A short toy workflow example is given in the example directory.

To run sisyphus on the example workflow change into the /example directory and run ../sis manager

A large realistic workflow will soon be added.

Development

If you want to commit to the repository make sure to run the unittest and check for PEP 8 by running tox. All need tools can be installed by running:

pip3 install -r requirements-dev.txt

To automatically check for PEP 8 errors before committing run:

pre-commit install

The unittest and flake8 on all relevant files is done by running tox:

tox

License

All Source Code in this Project is subject to the terms of the Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed with this file, You can obtain one at http://mozilla.org/MPL/2.0/.