Build a Docker container that mirrors the IVM's software stack. This is useful for providing a homogeneous environment in both the IVM and pipeline runner as well as allowing quicker testing of changes to the software deployment (i.e., before pushing it to Google Cloud and "hoping it works").
git clone --recursive https://github.com/wsi-hgi-tre/containerised-ivm-software.git
cd containerised-ivm-software
make
This will create a container named ivm-software, tagged with the
latest commit date of the Finngen codebase.
Note The Ansible run will take some time to complete; potentially several hours, depending on how much resource is available to the container.
Note The build process requires a non-trivial amount of memory; you may need to increase the resources available to your Docker containers, in virtualised environments (e.g., macOS), for the build to succeed.
The IVM's software stack is defined as IaC and will drift from this
repository. The submodule is set to track the sanger-production
branch, but it should be updated whenever the stack is updated and
pushed.
git submodule update --init --remote