CI	Branch	Build Status	Coverage
Docker	master
Travis	master
Travis	develop

This repository documents code used to gather, QC, standardize, and analyze data uploaded by centers participating in the VEO-IBD consortium.

These are tools or packages you will need, to be able to reproduce these results:

• Python 3.5 or higher

pip install git+https://github.com/veo-ibd/genie.git

This will install all the necessary components for you to run the validator locally on all of your files, including the Synapse client. Please view the help to see how to run to validator.

genie validate -h

1. Update the version in genie/version.py based on semantic versioning. Use the suffix -dev for development branch versions.
2. When releasing, remove the -dev from the version.
3. Add a tag and release named the same as the version.

1. Check docker hub builds to see if theres any failures
2. Log into AWS Batch
3. Run genie-job-mainprocess
4. Run genie-job-mafprocess (Make sure to add --createdMafDatabase flag)
5. Run genie-job-vcfprocess
6. Run genie-job-release (Make sure to update release version and number)

1. Input to database: input_to_database.py -h
2. Create Files

1. release 4.1-consortium and 4.0-public

   python database_to_staging.py Jan-2018 ~/cbioportal/ 4.1-consortium --skipMutationsInCis
   python consortium_to_public.py Jul-2018 ~/cbioportal/ 4.0-public

2. release 5.1-consortium and 5.0-public

   python database_to_staging.py Jul-2018 ~/cbioportal/ 5.1-consortium
   python consortium_to_public.py Jan-2019 ~/cbioportal/ 5.0-public

1. Build an AMI that can run batch jobs! Start from this page and follow instructions and specify your docker image. It is important at this stage that you time the building of your AMI, or your AMI will not be able to start batch jobs. After doing so, you will have to start an instance with the AMI and run these 2 commands:

   sudo stop ecs
   sudo rm -rf /var/lib/ecs/data/ecs_agent_data.json

2. Rebuild the AMI above, specify the size of the image and put whatever you want in the instance that you would want to bind

1. Invite users to VEO-IBD participant Team
2. Creates CENTER (input/staging) folder (Set up ACLs)
3. Update Center Mapping table https://www.synapse.org/#!Synapse:syn10061452/tables/
4. Add center to distribution tables: https://www.synapse.org/#!Synapse:syn10627220/tables/, https://www.synapse.org/#!Synapse:syn7268822/tables/
5. Add users to their VEO-IBD folder