Deployment

Cloud Infrastructure

_images/cloud.png

In a cloud infrasture, a head node is needed with ubuntu 18.04. Then we connect to the head node to

  1. Install Oxford Cats Software

  2. Start Oxford Cats Services

  3. Plug Pipelines

Install Cats Software

cd sp3doc
bash install.bash

Start Cats Services

cd sp3doc
bash systemd-start.sh

Plug Pipelines

  1. Clone pipeline code eg. to /data/pipelines/bug-flow

  2. Create sp3 configuration file for the pipeline, eg. bug-flow.yaml

  3. Add one line to ~/sp3/catweb/config.yaml Under the “nextflows:” add

"- !include config.yaml.d/davideyre/bug-flow.yaml"
  1. Copy singularity files to /data/images

  2. Copy references, other dependencies to /data/references

  3. Copy test data to /data/inputs/uploads/

  4. Restart catweb api and ui

systemctl restart catwebapi --user
systemctl restart catwebui --user