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orca-extended

Docker container for BioInformatics

This is an extension of https://github.com/bcgsc/orca to provide additional services and applications for running bioinformatics pipelines.

Additional programs:

  • 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.

Execution

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.

Logging in:

RStudio server: username orca, password orcauser Jupyter notebook: password orcauser