hiv-orderly OrderlyWeb configuration

For additional orderly documentation specific to the HIV deployment please see the wiki this contains information about sharepoint, and OW including how to update a package on the OW server.

Prerequisites

First, install the deploy tool

pip3 install --user orderly-web

Ensure that the path that the script is copied into is in your path (on Linux, most likely ~/.local/bin, on OSX ~/Library/Python/<version>/bin

Start

./start (all | <instance>..)

To start all instances

./start all

To start a specific instance

./start naomi

Notes

• The name needs to match the dir name in this repo, so for inference data it is inference_data
• The naomi instance starts the proxy which proxies all other instances at hiv-orderly.dide.ic.ac.uk/<instance>. When other instances are brought up we connect them to the proxy, because of this if you restart the naomi instance you must restart all other instances so they can connect to the new proxy.

Stop

./stop (all | <instance>...)

Upgrading

./stop (all | <instance>..)
./start (all | <instance>..)

Note that if you restart the naomi instance all other instances need to be restarted so they can be added to the proxy configuration.

Install a package

./orderly_install <instance> 'command'

e.g.

./orderly_install fertility "install.packages(\"dplyr\")"

Start an R session in the orderly container

./orderly_r <instance>

You can use this to then run things like orderly_pull_dependencies or orderly_pull_archive