BASiCSWorkflow

Bioconductor workflow to quantify and test changes in variability using BASiCS. This workflows runs using the docker image alanocallaghan/bocker. To use the latest build of the docker

docker pull alanocallaghan/basicsworkflow2020-docker

To run the docker image via Rstudio server. The code below ensures that the files in /home/rstudio/mycode are available within the docker.

make server

NOTE: for Macbook users with an M1 chip, the following WARNING will be returned:

WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested

To avoid that a --platform=linux/amd64 can be added:

docker run --platform=linux/amd64 -p 8787:8787 -v $(pwd):/home/rstudio/mycode -e PASSWORD=bioc alanocallaghan/basicsworkflow2020-docker

This issue has been documented by others e.g. here

Then access http://localhost:8787. Username: rstudio, password = bioc.

Equivalently, to launch bash:

make run