How to set up CSHL collection deployment in development mode

  • Make sure that you have read access to the directory with the collection data:

    ls -l /mnt/cephfs/seqpipe/duckdb_storage/

    If you can’t read the directory, ask the administrator to give you access.

  • Clone the CSHL collection deployment repository:

    git clone git@github.com:iossifovlab/cshl-collection-deployment.git

  • Enter into the repository directory and source the environment setup script:

    cd cshl-collection-deployment
source ./seqpipe_setenv.sh

  • Activate your GPF conda environment

  • Prepare to run the Django development server:

    • Run the migrations

      wdaemanage.py migrate

    • Create an admin user

      wdaemanage.py user_create admin@iossifovlab.com -p secret -g any_dataset:admin

    • Create an OAuth2 application for the frontend

      wdaemanage.py createapplication --user 1 \
    --redirect-uris "http://localhost:4200/login" \
    --name "GPF Genotypes and Phenotypes in Families" \
    --client-id gpfjs  public authorization-code --skip-authorization

    • Run the development server

      wdaemanage.py runserver

  • Enter into your GPFjs source directory and run the Angular development server

    cd gpfjs
npm install
ng serve

  • Open your browser and navigate to http://localhost:4200