gen3-augur

Access complete genomic sequence from gen3 data common https://chicagoland.pandemicresponsecommons.org (sequences originated from https://www.ncbi.nlm.nih.gov/genbank/sars-cov-2-seqs/). Create phylogenic tree using augur https://github.com/uc-cdis/augur (modified from https://github.com/nextstrain/augur).

Set GEN3_API_KEY

download credentials.json from commons
copy credentials.json $HOME/.gen3/credentials.json
export GEN3_API_KEY="$HOME/.gen3/credentials.json"

Specify Project id

export project_id="###"

Substitute "###" with your project id

Install gen3-client

• Download and unzip from: https://github.com/uc-cdis/cdis-data-client
• install gen3-client under the gen3/ folder

Using Conda

An environment.yml file is provided and can be used to build a virtual environment containing all dependencies. Create the environment using:

conda env create -f environment.yml

Then activate the environment for use:

conda activate gen3-augur

Install the gen3-augur package for use:

python setup.py develop

Run shell script

cd gen3-augur
mkdir data logs results auspice
bash gen3-augur-il.sh >> logs/run_pipeline.log

docker run

(
    IMAGE=quay.io/cdis/gen3-augur:fix_docker2;
    docker pull $IMAGE \
    && docker run --env https_proxy=http://cloud-proxy.internal.io:3128 --env http_proxy=http://cloud-proxy.internal.io:3128 --env no_proxy=localhost,127.0.0.1,169.254.169.254,.internal.io,logs.us-east-1.amazonaws.com,kibana.planx-pla.net -v $(pwd)/logs:/home/gen3/logs -v $(pwd)/results:/home/gen3/results -v $(pwd)/auspice:/home/gen3/auspice -v $(pwd)/data:/home/gen3/data -v $(pwd)/Gen3Secrets:/gen3 --rm --name=augurbatch $IMAGE
)

cp credential.json from local to container and cp auspice folder from container to local when run docker image

docker run -v ./credentials.json:/root/gen3-augur/config/ -v /root/gen3-augur/auspice/ ./ myimage