jvhoffbauer / sisyphus

A Workflow Manager in Python

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
pip3 install sphinxcontrib-mermaid

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

Known Problems:

• blocks may don't work correctly if used together with the async workflow

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/.