REAT is a robust easy-to-use genome annotation toolkit for turning high-quality genome assemblies into usable and informative resources. REAT makes use of state-of-the-art annotation tools and is robust to varying quality and sources of molecular evidence.
REAT provides an integrated environment that comprises both a set of workflows geared towards integrating multiple sources of evidence into a genome annotation, and an execution environment for these workflows.
To install REAT you can:
git clone https://github.com/ei-corebioinformatics/reat
wget https://github.com/broadinstitute/cromwell/releases/download/62/cromwell-62.jar
conda env create -f reat/reat.yml
pip install ./reatThese commands will download the cromwell binary required to execute the workflows and make REAT available in the 'reat' conda environment which can be activated using:
conda activate reatEach task in the workflow is configured with default resource requirements appropriate for most tasks, but these can be overriden by user provided ones. For examples of resource configuration files, refer to each module's description.
To configure the cromwell engine, there are two relevant files, the cromwell runtime options and the workflow options files.
The cromwell engine can be configured to run in your environment using a file such as:
none
The workflow options can be used to activate the caching behaviour in cromwell, i.e:
modules/transcriptome/index modules/homology/index modules/prediction/index
genindexmodindexsearch