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CeNDR

CeNDR is the code used to run the Caenorhabditis elegans Natural Diversity Resource website.

cendr website

Page versions

  • download_tab_isotype_v1.html - references the original download table which links to isotype-level bams

  • download_tab_strain_v2.html - references the new CeNDR versions which organize sequence data at the strain level.

Building the static database

Initializing the database

You can create the CeNDR database by running:

flask initdb WS276 # Where WS276 is the version of wormbase

Running the docker container

docker build -t cendr .
GAE_VERSION=`cat .travis.yml  | grep 'export VERSION' | cut -f 2 -d '=' | sed 's/version-//g' | awk '{gsub("-", ".", $0); print}'`
# Doesn't require rebuilding
docker run -it -v $PWD:/home/vmagent/app -e GOOGLE_APPLICATION_CREDENTIALS=client-secret.json -e APP_CONFIG=debug -e GAE_VERSION=${GAE_VERSION} --publish $PORT:$PORT cendr /bin/bash
gunicorn -b :$PORT main:app