sifbuilder facilitates the building of NMRbox based Apptainer containers. Software can be specified either as NMRbox Software entries or debian package names. The most current versions will be used if no version is specified.
Check out project, create virtual environment and run pip install -e . from top level directory in virtual environment.
e.g. python3 -m venv venv
./venv/bin.pip install -e .
See the example.yaml.
sifbuilder -h lists runtime options. The basic syntax pattern is:
- sifbuilder myconfig.yaml generate (produces def file specified in yaml)
- sifbuilder myconfig.yaml sif (generates sif file from def file)
This allows hand editing of the def file before building the environment.
For debugging environments, sifbuilder myconfig.yaml sandbox is also supported.
--force to overwrite def or sif files.
by default, the verbose output of Apptainer build commands goes to a file, --nolog will stream Apptainer output
directly to stdout / stderr.
--loglevel [Python level] adds some debug output
Apptainer exec can be used to run a command or script inside the container. See the bind option for how to make host directories available in the container.
Supporting NMRbox paths from outside the container is not straightforward.
- consider installing the nmrbox-paths-paas or nmrbox-paths-download package, or
- use full paths names in scripts
By default the environment accessed by Apptainer exec is does not source PATH commands
(it is not an "interactive" shell). Writing a script that starts with
#!/bin/bash -i
will make the shell interactive. If not embedded in the container, the script must be on a path the container binds to
by default (e.g. /tmp) or explicitly with -bind option.
This module is under development pending user feedback.