Skip to content
Core functionality of the CGAT code
Branch: master
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Type Name Latest commit message Commit time
Failed to load latest commit information.
cgatcore Merge pull request #94 from cgat-developers/AC-sftp Jul 2, 2019
conda/environments updated conda requirements Jun 28, 2019
docs Update Tutorial.rst Jul 12, 2019
scripts python-drmaa is no longer available as a conda package (#81) Mar 10, 2019
tests {AH} increase version to 0.5.11 Mar 10, 2019
.gitignore added gitignore for hash files Jun 2, 2019
Dockerfile added docker file Jul 3, 2019
INSTALL {AH,SLV,AC} first import Oct 27, 2017
LICENSE {AH} change CGATCore to cgatcore Sep 13, 2018 Update README Mar 19, 2019
THANKS.txt include thanks.txt Feb 16, 2018
readthedocs.yml typo Feb 21, 2019


CGAT-core is a workflow management system that allows users to quickly and reproducibly build scalable data analysis pipelines. CGAT-core is a set of libraries and helper functions used to enable researchers to design and build computational workflows for the analysis of large-scale data-analysis.

Documentation for CGAT-core can be accessed at read the docs

Used in combination with CGAT-apps, we have demonstrated the functionality of our flexible implementation using a set of well documented, easy to install and easy to use workflows, called CGAT-flow (Documentation).

CGAT-core is open-sourced, powerful and user-friendly, and has been continually developed as a Next Generation Sequencing (NGS) workflow management system over the past 10 years.


The following sections describe how to install the cgatcore framework. For instructions on how to install our other repos, CGAT-apps (scripts) and CGAT-flow (workflows/pipelines), please follow these instructions here.

The preferred method to install the cgatcore is using conda, by following the instructions on read the docs. However, there are a few other methods to install cgatcore, including pip and our own bash script installer.

Linux vs OS X

  • ulimit works as expected in Linux but it does not have an effect on OS X. Disabled ulimit tests for OS X.

  • ssh.connect times out in OSX. Exception caught

  • Linux uses /proc/meminfo and OS X uses vm_stat

  • Currently our testing framework is broken for OSX, however we are working to fix this. However, we dont envisage any issues running the code at present.

You can’t perform that action at this time.