Using the Container¶
Invoking a shell inside the container¶
To invoke a shell session inside the container:
# Docker command docker run -it immcantation/suite:devel bash # Singularity command singularity shell immcantation_suite-devel.sif
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
$HOME/project mounted to
# Docker command docker run -v $HOME/project:/data:z immcantation/suite:devel 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 provided details about the versions of installed software and available pipelines.
versions report command which will inspect the installed software
versions and print them to standard output.
There is an analagous
builds report command to display the build date and
changesets used during the image build. This is particularly relevant if you
are using the
immcantation/suite:devel development builds.
pipelines report command will display a list of available template
pipelines included in the container.