Bioinformatics pipelines for the Resolwe dataflow package for Django framework.
Read about getting started and how to write processes in the documentation.
To chat with developers or ask for help, join us on Slack.
Make sure you have Python 3.6 installed on your system. If you don't have it yet, follow these instructions.
Resolwe requires PostgreSQL (9.4+). Many Linux distributions already include the required version of PostgreSQL (e.g. Fedora 22+, Debian 8+, Ubuntu 15.04+) and you can simply install it via distribution's package manager. Otherwise, follow these instructions.
Additionally, installing some (indirect) dependencies from PyPI will require having a C compiler (e.g. GCC) as well as Python development files installed on the system.
The preferred way to install the C compiler and Python development files is to
use your distribution's packages, if they exist. For example, on a
Fedora/RHEL-based system, that would mean installing gcc and
python3-devel packages.
Using PyPI
pip install resolwe-bio
To install a pre-release, use:
pip install --pre resolwe-bio
Using source on GitHub
pip install --pre https://github.com/genialis/resolwe-bio/archive/<git-tree-ish>.tar.gz
where <git-tree-ish> can represent any commit SHA, branch name, tag name,
etc. in Resolwe Bioinformatics' GitHub repository. For example, to install
the latest Resolwe Bioinformatics from the master branch, use:
pip install --pre https://github.com/genialis/resolwe-bio/archive/master.tar.gz
We welcome new contributors. To learn more, read Contributing section of the documentation.