Running Locally
The CAMRA pipeline is based on the workflow description language (wdl). This language allows for easy management of workflow inputs, tasks, and outputs. These wdls utilize docker containers to run various tools without needing to install them directly.
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Unix/Linux OS (Tested on MacOS and Ubuntu)
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Cromwell - Install Docs
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Wombat - Install Docs
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Java 17 or later runtime environment - Download
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Docker - Download
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BV-BRC Account - More Information
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Clone the repository
git clone https://github.com/JCVenterInstitute/CAMRA
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Create input JSON file. (See workflow description section for templates)
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To run a workflow use the command:
java -jar /path/to/cromwell-87.jar run --inputs /path/to/input.json /path/to/workflow.wdl