A dockerfile to set up all the software dependencies necessary to run Kamvar et al. 2017.
Note that this container does not contain any of the code or data from Kamvar et al. 2017, it is simply the computational environment for the code. The code and data can be found at https://github.com/everhartlab/sclerotinia-366 or on the Open Science Framework at https://osf.io/ejb5y/ (github is easier to browse, but the OSF project is more permanent). All versions of the container are synced on Docker hub: https://hub.docker.com/r/everhartlab/sclerotinia-366-dependencies/
The image can be run via the command line. Docker will automatically install the image for you.
docker run --rm --name ssc-dep -dp 8787:8787 -e ROOT=TRUE everhartlab/sclerotinia-366-dependencies:latest
After that finishes, you can open your browser to localhost:8787 and log in with
- Username: rstudio
- Password: rstudio
When you are finished, you can stop the container with:
docker stop ssc-dep
Kamvar et al. is rebuilt whenever something changes in the code. You can run the container that contains all the code and data like so:
docker run --rm --name ssc -dp 8787:8787 -e ROOT=TRUE everhartlab/sclerotinia-366
After you open Rstudio server, you should open the Terminal tab and use
cp -R /analysis . to copy the code and data to the current working directory.
If you want to use it to rebuild Kamvar et al. 2017 from scratch , you can do the following:
git clone https://github.com/everhartlab/sclerotinia-366.git
cd sclerotinia-366
docker run --rm --name ssc-dep -dp 8787:8787 -v $(pwd):/home/rstudio/ -e ROOT=TRUE everhartlab/sclerotinia-366-dependencies