/viva-docker

Primary LanguageShell

VIVA Install instructions

  • Install git, docker-engine and docker-compose
  • Run prepare.sh to clone appropriate repos.
  • The following files will need to be adapted to the environment (the default is localhost):
    1. nginx/conf.d/viva.conf
    2. viva_metadata/cpgmeta/local_settings.py
    3. viva_publicapi/public_api/public_api/settings/local.py
    4. viva_varkb/varkb_vw/settings/local.py
    5. viva_ui/config/environment.js
    6. docker-compose.yml, docker-compose.proxy.yml and docker-compose.dev.yml depending on environment
  • Run docker-compose up --build
  • The default configs should be enough to setup a running instance of VIVA on http://localhost:8080 on the host machine

VIVA UI development

  • Install git, docker-engine and docker-compose
  • Run prepare.sh to clone appropriate repos.
  • Run setup_dbs.sh to setup the databases.
  • Follow viva_ui/README.md instructions for dev with docker-sync
  • Or for running tests you can run this command:
    1. docker-compose -f docker-compose.yml -f docker-compose.dev.yml -f docker-compose.ui-test.yml run --rm viva_ui

To install an independent instance for development:

  1. dump data from metadata postgres database to ./fixtures/metadata.pgdump. The dump command should be along the lines of:

    $ pg_dump -Fc -h host -U user -d db > <filename>.metadump

  2. dump data from varkb postgres database to ./fixtures/varkb.pgdump. The dump command should be along the lines of:

    $ pg_dump -Fc -h host -U user -d db -t core_* -T core_call -T core_variantjoin
    • Notice table core_call table being skipped

  3. subset the core_call table from the varkb postgres db to ./fixtures/varkb_calls.gz along the following lines:

    $ psql -h host -U user db -c "\copy (select * from core_call where sample in ('1','2','3','4','5','6','7','8','9','10')) to STDOUT with binary" | gzip > varkb_calls.gz