pipeline.cache

pipeline.cache

Functions for singularity cache management

Functions

Name	Description
check_cache	Check if provided SINGULARITY_CACHE is valid. Singularity caches cannot be
get_singularity_cachedir	Returns the singularity cache directory.
image_cache	Adds Docker Image URIs, or SIF paths to config if singularity cache option is provided.

check_cache

pipeline.cache.check_cache(parser, cache, *args, **kwargs)

Check if provided SINGULARITY_CACHE is valid. Singularity caches cannot be shared across users (and must be owned by the user). Singularity strictly enforces 0700 user permission on on the cache directory and will return a non-zero exitcode. @param parser <argparse.ArgumentParser() object>: Argparse parser object @param cache : Singularity cache directory @return cache : If singularity cache dir is valid

get_singularity_cachedir

pipeline.cache.get_singularity_cachedir(output_dir=None, cache_dir=None)

Returns the singularity cache directory. If no user-provided cache directory is provided, the default singularity cache is in the output directory.

image_cache

pipeline.cache.image_cache(sub_args, config)

Adds Docker Image URIs, or SIF paths to config if singularity cache option is provided. If singularity cache option is provided and a local SIF does not exist, a warning is displayed and the image will be pulled from URI in ‘config/containers/images.json’. @param sub_args <parser.parse_args() object>: Parsed arguments for run sub-command @params config : Docker Image config file @return config : Updated config dictionary containing user information (username and home directory)