To build a docker container do ./build_container.sh
To run docker container do ./run_container.sh
It emits a password for Rstudio, use it to log in on localhost:8787
When in Rstudio, run the script preproc.R
Once finished, use data_upload_script.ipynb to upload the data to s3
Run it in a folder with all the required files: cells_output.tsv, genes_output.tsv, normalized.mtx, raw.mtx.
Before you use the data_upload_script.ipynb, set up your aws config so it points to the right region:
aws configure set default.region eu-west-1
Make sure that your aws credentials file has the correct credentials