Docker container for BioInformatics
This is an extension of https://github.com/bcgsc/orca to provide additional services and applications for running bioinformatics pipelines.
- jupyter
- deepTools
- macs2
- htseq
- homer (including mm10 genome)
- rstudio-server
It also includes a number of R packages useful for carrying out analysis. See install.R for a list of these.
From source:
docker build -t orcaext .
docker run -p 8787:8787 -p 8888:8888 -v $HOME:$HOME -w $HOME orcaext
This will expose RStudio server on port 8787 and jupyter notebook on port 8888
Please note that it takes a very long time to build and install the R packages so it is only recommended to build this container once per release from source.
RStudio server: username orca, password orcauser
Jupyter notebook: password orcauser