Skip to content

docker: bash kernel fix

Latest
Latest
Compare
Choose a tag to compare
@trstickland trstickland released this 08 Aug 09:21
· 35 commits to master since this release
RT666608
69370a9
This commit was created on GitHub.com and signed with GitHub’s verified signature. The key has expired.
GPG key ID: 4AEE18F83AFDEB23
Expired
Learn about vigilant mode.
  • 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
Assets 2
Loading