C. Install package

Clone the submission pipeline repository and pull the prebuilt container images from GitHub Container Registry.

Requires: GitHub access (step B)

make pull authenticates via the read:packages scope added in the previous step. Complete B. GitHub access before continuing.

1. Clone the repository

Windows: use Git Bash

Open Git Bash (installed with Git for Windows in step A). All make commands in this manual must be run in Git Bash, not PowerShell.

git clone --recurse-submodules https://github.com/imi-bigpicture/bp-submission-pipeline.git
cd bp-submission-pipeline
What are submodules?

The pipeline bundles several companion components (web app, data model, and submission CLI) as Git submodules — without --recurse-submodules those folders arrive empty and the pipeline will not start.

Verify 
ls bigpicture-metadata-interface

You should see files listed inside the folder, not an empty directory.

You are now inside bp-submission-pipeline/

All commands from here through step J are run from this directory. If you open a new terminal, run cd bp-submission-pipeline before continuing.

2. Pull the container images

make pull
Verify 
docker image ls | grep ghcr.io/imi-bigpicture/bp-submission-pipeline

Expected: one or more ghcr.io/imi-bigpicture/bp-submission-pipeline/... images listed.

If something goes wrong

make pull fails with “lacks the read:packages scope”

Return to B. GitHub access and run gh auth refresh -s read:packages, then try again.

Clone fails with “repository not found” or “access denied”

Your GitHub account has not been granted access to the private repository. Request access via the servicedesk.

make pull fails with “no such file or directory” on /var/run/docker.sock

The Docker daemon is not running. Start it and retry:

Launch Docker Desktop and wait until the whale icon in the taskbar/menu bar shows “Docker Desktop is running”, then run make pull again.

systemctl start docker

On older systems without systemd, use service docker start instead. Then run make pull again.

Submodule folders are empty after cloning

You cloned without --recurse-submodules. Delete the cloned folder and re-run the full clone command above.