Prerequisites

Platform: ODAP

Since the data is sensitive, it is meant to run on the ODAP platform (at least for now). To get access, you will need to contact the relevant person, at the moment dominique.mccormick@ed.ac.uk. More information on accessing ODAP can be found here.

Software

In order to run the workflows in this repository only 2 software need to be installed, and they should already be present on ODAP:

Nextflow 24.10.3 (see how to setup)
Singularity 3.9.4 (Should be ready to use)

Importing Into ODAP

In order to upload the current state of the code, or a specific version of FlowOMICC into ODAP, we currently proceed via a shared folder with Dominique.

Locally

The following assumes a specific git tag corresponding to a release for which a matching docker image exists, but the steps can be adapted to any need.

export FLOWOMICC_TAG="main"

In the shared folder.

Clone the repository or the relevant commit or tag:

git clone git@github.com:baillielab/sequential-gwas.git
git checkout $FLOWOMICC_TAG

Download and save the docker image

docker pull --platform linux/amd64 olivierlabayle/genomicc:$FLOWOMICC_TAG
docker save olivierlabayle/genomicc:$FLOWOMICC_TAG | gzip > sequential-gwas/genomicc.tar.gz

Then ask Dominique to uplaod the folder to ODAP.

On ODAP

In the uploaded repository, build the singularity image:

gunzip genomicc.tar.gz && singularity build genomicc.sif docker-archive:genomicc.tar