waldronlab/wallabe-release repository overview

⁠wallabe-release

The wallabe-release Docker container is a custom container built on top of the waldronlab/bioconductor container. It differs in two principle ways: 1) the /usr/local/lib/R/site-library directory is writeable to all users and 2) host user directories are mounted into the container with the correct permissions and ownership (provided the invocation below is followed).

The first item above is achieved through revisions to the s6 overlay /etc/fix-attrs.d/00-runscripts ownership and permissions script. The second item above is achieved by invoking the container with a bash script as follows and then correcting ownership and permissions with another s6 overlay script at /etc/cont-init.d/userconf during the init process. It is necessary to change the user directory ownership and permissions during the init process, rather than in the /etc/fix-attrs.d/00-runscripts script, because user directories are not mounted (and their structure cannot be assumed prior to) the starting to the container.

#!/bin/bash
wallabe_volumes="-v /etc/passwd:/etc/passwd:ro\
                 -v /etc/group:/etc/group:ro\
                 -v /etc/shadow:/etc/shadow:ro\
                 -v /etc/pam.d/login:/etc/pam.d/login:ro\
                 -v /data:/data"

directories="Desktop Documents Downloads .gitconfig .github Music Pictures\
             Public Videos"

for i in $(ls /home/); do
  if [[ $(stat -c "%u" /home/${i}/) < 1001 ]]; then
    continue;
  fi
  if [[ $(stat -c "%U" /home/${i}/) == "UNKNOWN" ]]; then
    continue;
  fi
  for j in $directories; do
    wallabe_volumes+=" -v /home/${i}/${j}:/home/${i}/${j}"
  done
done

docker pull waldronlab/wallabe-release
docker stop wallabe-release
docker rm wallabe-release

docker run -d --name wallabe-release --restart unless-stopped -p 7000:8787 \
  $wallabe_volumes waldronlab/wallabe-release

Complete information about the just containers s6 overlay is available here⁠. Or a really deep dive is available here⁠.