Deploying GeneNetwork CD

Prerequisites

Ensure you have `fzf' installed and Guix is set up with your preferred channel configuration.

Step 1: Pull the Latest Profiles

guix pull -C channels.scm -p ~/.guix-extra-profiles/gn-machines --allow-downgrades
guix pull -C channels.scm -p ~/.guix-extra-profiles/gn-machines-shepherd-upgrade --allow-downgrades

Step 2: Source the Correct Profile

. ,choose-profile

Contents of `,choose-profile'

This script lets you interactively select a profile using `fzf':

#!/bin/env sh

export GUIX_PROFILE="$(guix package --list-profiles | fzf --multi)"
. "$GUIX_PROFILE/etc/profile"

hash guix

echo "Currently using: $GUIX_PROFILE"

Step 3: Verify the Profile

guix describe

Step 4: Pull the Latest Code

cd gn-machines
git pull

Step 5: Run the Deployment Script

./genenetwork-development-deploy.sh

Step 6: Restart the Development Container

sudo systemctl restart genenetwork-development-container

Step 7: Verify Changes

Manually confirm that the intended changes were applied correctly.

Accessing the Development Container on tux02

To enter the running container shell, ensure you're using the *parent* PID of the `shepherd' process.

Step 1: Identify the Correct PID

Use this command to locate the correct container parent process:

ps -u root -f --forest | grep -A4 '/usr/local/bin/genenetwork-development-container' | grep shepherd

Step 2: Enter the Container

Replace `46804' with your actual parent PID:

sudo /home/bonfacem/.config/guix/current/bin/guix container exec 46804 \
  /gnu/store/m6c5hgqg569mbcjjbp8l8m7q82ascpdl-bash-5.1.16/bin/bash \
  --init-file /home/bonfacem/.guix-profile/etc/profile --login

Notes

Ensure the PID is the container’s *shepherd parent*, not a child process.
Always double-check your environment and profiles before deploying.