Using the Container¶
Invoking a shell inside the container¶
To invoke a shell session inside the container:
# Docker command docker run -it immcantation/suite:4.4.0 bash # Singularity command singularity shell immcantation_suite-4.4.0.sif
Sharing files with the container¶
Sharing files between the host operating system and the container requires you
to bind a directory on the host to one of the container’s mount points using the
-v
argument for docker
or the -B
argument for singularity
.
There are four available mount points defined in the container:
/data
/scratch
/software
/oasis
For example, to invoke a shell session inside the container with $HOME/project
mounted to
/data
:
# Docker command docker run -it -v $HOME/project:/data:z immcantation/suite:4.4.0 bash # Singularity command singularity shell -B $HOME/project:/data immcantation_suite-4.4.0.sif
Note, the :z
in the -v
argument of the docker
command is essential.
Executing a specific command¶
After invoking an interactive session inside the container, commands can be executed in the container shell as they would be executed in the host shell.
Alternatively, it is possible to execute a specific command directly inside the
container without starting an interactive session. The next example demonstrates
how to execute ls
within $HOME/project
mounted to /data
:
# Docker command docker run -v $HOME/project:/data:z immcantation/suite:4.4.0 ls /data # Singularity command singularity exec -B $HOME/project:/data immcantation_suite_|docker-version|.sif ls /data
Inspecting the container components¶
The container includes three informational scripts that provide details about the versions of installed software and available pipelines.
The
versions report
command will inspect the installed software versions and print them to standard output.The analagous
builds report
command will display the build date and changesets used during the image build. This is particularly relevant if you are using theimmcantation/suite:devel
development builds.Finally, the
pipelines report
command will display a list of available template pipelines included in the container.
Each command can be run using:
# Docker command docker run immcantation/suite:4.4.0 [command] # Singularity command singularity exec immcantation_suite_|docker-version|.sif [command]