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Brian Haas edited this page Jul 7, 2018 · 4 revisions

Running the Single Cell Workshop Practicals Locally

Note, this is not for running during the ISMB workshop, as it involves downloading a number of large files and it will deplete the bandwidth available. Best to do this from home or from your workplace.

The practicals involve using Rstudio having the single cell software all installed along with access to the tutorial data sets.

For this to work, you must have Docker installed. Visit https://www.docker.com/ to download and install docker.

Once Docker is running, you can perform the following operations to begin:

 # pull the docker image:
 docker pull trinityctat/scellismb2018
 
 # download the tutorial data set:
 wget https://data.broadinstitute.org/Trinity/RNASEQ_WORKSHOP/ismb_sc2018.pbmcs.tar.gz

 # unpack the data
 tar xvf ismb_sc2018.pbmcs.tar.gz

 # Run docker
  docker run --rm -it -v $PWD/shared_ro:/home/training/shared_ro:ro -p 8787:8787 trinityctat/scellismb2018

and then visit the following link in your web browser:

http://localhost:8787

The user/password will be the same you used during the on-site workshop (training/training).

To stop the docker, type cntrl-c in the terminal window that has the instance running.

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