diff --git a/bih-cluster/docs/how-to/software/apptainer.md b/bih-cluster/docs/how-to/software/apptainer.md index 7515d4a2a..61321a842 100644 --- a/bih-cluster/docs/how-to/software/apptainer.md +++ b/bih-cluster/docs/how-to/software/apptainer.md @@ -39,7 +39,7 @@ The following guide gives a quick dive into using docker images with apptainer. Run a bash in a docker image: ```bash -host:~$ apptainer bash docker://godlovedc/lolcow +host:~$ apptainer shell docker://godlovedc/lolcow ``` Run a command in a docker image: @@ -51,7 +51,7 @@ host:~$ apptainer exec docker://godlovedc/lolcow echo "hello, hello!" Run a bash in a docker image, enable access to the cuda driver (--nv) and mount a path (--bind or -B): ```bash -host:~$ apptainer bash --nv --bind /path_on_host/:/path_inside_container/ docker://godlovedc/lolcow +host:~$ apptainer shell --nv --bind /path_on_host/:/path_inside_container/ docker://godlovedc/lolcow ``` ## Some Caveats and Notes @@ -65,7 +65,7 @@ host:~$ apptainer bash --nv --bind /path_on_host/:/path_inside_container/ docker - Environment variables can be provided by setting them in the bash and adding the prefix `APPTAINERENV_`: ```bash - host:~$ APPTAINERENV_HELLO=123 apptainer bash docker://godlovedc/lolcow echo $HELLO + host:~$ APPTAINERENV_HELLO=123 apptainer shell docker://godlovedc/lolcow echo $HELLO ``` - Calling `apptainer shell` or `apptainer exec` uses as cwd the host callers cwd not the one set in the Dockerfile. One can change this by setting `--pwd`. @@ -84,7 +84,7 @@ host:~$ apptainer run docker://godlovedc/lolcow or to open a shell inside the image ```bash -host:~$ apptainer bash docker://godlovedc/lolcow +host:~$ apptainer shell docker://godlovedc/lolcow ``` Furthermore, similar to docker, one can pull (and convert) remote image with the following call: