How to get a new Docker image to Sandbox

Docker containers enable you to roll up all the files and other dependencies needed to run an application/tool in a separate system isolated from all other processes on your computer. A container image refers to a file system holding these necessary folders and files.

To learn more about Docker visit Docker get started page and see Docker tutorial video.

If you want to run a tool in your sandbox that might require the installation and assembly of many files, then we offer you the option to import and run it as a Docker container.

To access Docker, open Terminal Emulator from the Application dropdown menu at Sandbox desktop. To see all Docker commands and options available, type

:~$ docker --help

To see options for pull command

:~$ docker pull --help

To pull an image or a repository from a registry

:~$ docker pull path/to/repository

An example:

:~$ docker pull eu.gcr.io/finngen-sandbox-v3-containers/bioinformatics:1.0.1

To list Docker images

:~$ docker images

REPOSITORY             TAG       IMAGE ID       CREATED       SIZE
path/to/repository     1.0.1      i1m2a3g4e5   2 years ago    3.91GB

Assign a name (here "tools") to the container and run Docker container in background (-d option) keeping STDIN open (-i option) and allocating a pseudo-TTY (-t option)

:~$ docker run -dit --name tools i1m2a3g4e5

To list containers those are running

:~$ docker ps

CONTAINER ID   IMAGE           COMMAND      CREATED          STATUS          PORTS     NAMES
c1on2ta3ine4r   i1m2a3g4e5   "/bin/bash"   3 minutes ago   Up 3 minutes                tools

To stop container

:~$ docker stop tools

To list stopped containers

:~$ docker ps -a

CONTAINER ID   IMAGE          COMMAND       CREATED         STATUS                          PORTS        NAMES
c1on2ta3ine4r   i1m2a3g4e5   "/bin/bash"   4 minutes ago   Exited (0) About a minute ago    tools

To start the run again

:~$ docker start tools

To attach local standard input, output and error streams to a running container image

:~$ docker attach tools

returns (if nothing seems to happen press enter again):

root@01r23o45o67t:/#

List folders in the container

:/# ls

bin  boot  dev  etc  home  lib  lib32  lib64  liftover  media  mnt  opt  proc  root  run  sbin  srv  sys  tmp  usr  var

You can enter a folder typing cd folder_name e.g.

:/# cd home

To go back to the upper folder

:/# cd ..

Check that plink is runnable within the image:

:/# plink

PLINK v1.90b6.9 64-bit (4 Mar 2019)            www.cog-genomics.org/plink/1.9/
(C) 2005-2019 Shaun Purcell, Christopher Chang   GNU General Public License v3
  plink <input flag(s)...> [command flag(s)...] [other flag(s)...]
  plink --help [flag name(s)...]
Commands include --make-bed, --recode, --flip-scan, --merge-list,
--write-snplist, --list-duplicate-vars, --freqx, --missing, --test-mishap,
--hardy, --mendel, --ibc, --impute-sex, --indep-pairphase, --r2, --show-tags,
--blocks, --distance, --genome, --homozyg, --make-rel, --make-grm-gz,
--rel-cutoff, --cluster, --pca, --neighbour, --ibs-test, --regress-distance,
--model, --bd, --gxe, --logistic, --dosage, --lasso, --test-missing,
--make-perm-pheno, --tdt, --qfam, --annotate, --clump, --gene-report,
--meta-analysis, --epistasis, --fast-epistasis, and --score.
'plink --help | more' describes all functions (warning: long).

To exit from the image

:/# exit

List stopped containers

:~$ docker ps -a

CONTAINER ID   IMAGE          COMMAND       CREATED         STATUS                          PORTS        NAMES
c1on2ta3ine4r   i1m2a3g4e5   "/bin/bash"   10 minutes ago   Exited (0) About a minute ago    tools

Remove container

:~$ docker rm tools

Check that container is removed

:~$ docker ps -a

CONTAINER ID   IMAGE          COMMAND       CREATED         STATUS                          PORTS        NAMES

Remove the image

:~$ docker rmi i1m2a3g4e5