resolwe-bio 1.0.0

Bioinformatics pipelines for the Resolwe platform.

Bioinformatics pipelines for the Resolwe dataflow package for Django framework.

Docs & Help

Read about getting started and how to write processes in the documentation.

To chat with developers or ask for help, join us on Slack.

Install

Prerequisites

Make sure you have Python (2.7 or 3.4+) 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 the psycopg2 dependency from PyPI will require having a C compiler (e.g. GCC) as well as Python and PostgreSQL development files installed on the system.

Note

The preferred way to install the C compiler and Python and PostgreSQL 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, python-devel/python3-devel and postgresql-devel packages.

From PyPI

pip install resolwe-bio

From source

pip install 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 https://github.com/genialis/resolwe-bio/archive/master.tar.gz

Contribute

We welcome new contributors. To learn more, read Contributing section of the documentation.