mahlaranjeet / cgat-core

Core functionality of the CGAT code

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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.

Installation

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.