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 provide details about the versions of installed software and available pipelines.
versions reportcommand will inspect the installed software versions and print them to standard output.
builds reportcommand will display the build date and changesets used during the image build. This is particularly relevant if you are using the
pipelines reportcommand will display a list of available template pipelines included in the container.
Each command can be run using:
# Docker command docker run immcantation/suite:devel [command] # Singularity command singularity exec immcantation_suite_|docker-version|.sif [command]