ODAP

The original GenOMICC data is kept on the ODAP platform. 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 (see how to setup)
Singularity (Should be ready to use)

Importing Into ODAP

In order to upload the current state of the code, or a specific version of genomicc-workflows 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 genomicc_workflows_tag="0.1.0"

In the shared folder.

Clone the repository or the relevant commit or tag:

git clone git@github.com:baillielab/genomicc-workflows.git
cd genomicc-workflows
git checkout v$genomicc_workflows_tag

Download and save the docker image

docker pull --platform linux/amd64 olivierlabayle/genomicc:$genomicc_workflows_tag
docker save olivierlabayle/genomicc:$genomicc_workflows_tag | gzip > 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