Pathogen Informatics Training Versions Save

• addresses docker image issues RT666607 and RT666608
• bash kernel OK with the AToW latest jupyter/scipy-notebook (58169ec3cfd3)
• Dockerfile specifies base image tag (:58169ec3cfd3) to help prevent nasty surprises like this recurring
• the build was broken with this base image, but managed to get it working by installing as many dependencies as possible from Ubuntu packages, and pip install for SeroBA; bioconda now used only for the prokka install
• also replaced git clone with a COPY in the docker build, so the notebooks are those from the current repo -- doing a clone means the docker build always uses notebooks from the current master branch in sanger-pathogens repo -- doing a COPY will use notebooks from whatever branch/tag/fork the user has checked out -- this is essential for DockerHub automated builds on branches and tags to work as expected

Release of the training notebooks to be used in the Joberg NGS Bioinformatics course Feb 2019

Used for Wellcome Trust Genome Campus advanced course NGS Bioinformatics October 2017