A virtual interactive computing environment (VICE) for Tiny Earth Genomics

This Dockerfile is designed to be used with Cyverse, although you can also use it locally through a browser, as part of the Tiny Earth Genomics course. It has the following bioinformatics tools installed:

• AntiSMASH (For finding and annotating secondary metabolite pathways)
• Barrnap (For finding ribosomal RNA genes in genomes)
• BiG-SCAPE (For comparing antismash results)
• Clinker (For fine-grain comparisons of BGCs)
• DIAMOND (For searching for similar proteins)
• KofamScan (For sorting genes into functional categories)
• Prokka (For annotating bacterial genomes)

It also has the following R packages installed:

• ggalluvial
• ggplot2
• grid
• plotly
• reshape2
• vegan
• viridis

If you would like to run the Docker image locally, first build or pull the image from Dockerhub, then run the following command:

docker run -it --rm -v /$HOME:/work --workdir /work -p 8888:8888 -e REDIRECT_URL=http://localhost:8888 jasonkwan/tiny_earth_vice:latest

Then, you should be able to interact with the image by navigating to http://localhost:8888 in your browser. Note: In the example above, the working directory for the image will be your $HOME directory. Change this to whatever you want to use.