====== Docker ======

Docker containers are one way of establishing a fixed software environment. This is ideal for sharing the exact version and setup used for running your project.

===== Using =====
see [[https://fmriprep.org/en/20.2.0/docker.html|fmriprep's docker documenation]]

==== Hints ====

  * Use bind mounts to map an actual path to a virtual one within the container like ''-v /abs/actual/path:/path/in/container''
    * bind mount files that might otherwise be downloaded and discarded like [[:tools:templateflow]].
  * use ''%%--user%%'' to not run as root. ''%%--user $(id -u):$(id -g)%%''. w/o user, containers may run as root and 
  * export variables for your local environment to the container like ''%%--env FS_LICSENSE%%''
    * combine with bind mount <code bash rundocker.bash>docker run -v $FS_LICENSE:$FS_LICENSE --env FS_LICENSE freesurfer/freesurfer </code>
  * use ''%%--entrypoint%%'' to change what gets run. eg ''%%-it --entrypoint bash%%'' for debugging.
===== Creating =====

see [[https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008316|Ten simple rules for writing Dockerfiles for reproducible data science]]

===== On rhea =====

on [[admin:it:rhea]], docker containers are stored in ''/home/ni_tools/docker'' replacing the default folder ''/var/lib/docker'' with a symbolic link

<code>
ls -l  /var/lib/docker
lrwxrwxrwx 1 root root 21 Apr 18  2018 /var/lib/docker -> /home/ni_tools/docker

 df -h /home
Filesystem      Size  Used Avail Use% Mounted on
/dev/sdc2       3.4T  952G  2.3T  30% /home
</code>