grr_cache_repo

grr_cache_repo downloads the resources that an annotation pipeline uses into the GRR cache. It reads the pipeline, a file or a GRR resource id, and the GRR definition. It writes a copy of each resource of the pipeline into the cache_dir of the GRR definition. Use it before a large annotation job, so that the job reads local copies and does not stop to download resources.

Examples

grr_cache_repo pipeline/hg38_clinical_annotation

Caches the resources of the pipeline/hg38_clinical_annotation pipeline resource.

grr_cache_repo -g my_grr_definition.yaml -j 8 custom_pipeline.yaml

Caches the resources of a pipeline file with 8 parallel downloads, into the cache that my_grr_definition.yaml configures.

See also

• Caching resources: set up a cache and annotate from it.

• Resource caching: the cache_dir entry of a GRR definition.

Option reference

Cache the genomic resources used by an annotation pipeline.

usage: grr_cache_repo [-h] [--jobs JOBS] [--no-progress] [-g GRR_FILENAME]
                      [--grr-directory GRR_DIRECTORY]
                      [-R REFERENCE_GENOME_RESOURCE_ID]
                      [-G GENE_MODELS_RESOURCE_ID] [-ar] [--verbose]
                      [--logfile LOGFILE]
                      [pipeline]

Positional Arguments

pipeline

The pipeline definition file. By default, or if the value is gpf_instance, the annotation pipeline from the configured gpf instance will be used.

Default: 'context'

Named Arguments

--jobs, -j

Number of parallel workers fetching resources.

Default: 4

--no-progress

Disable the progress indication (live bar on a terminal, milestone log lines otherwise).

Default: True

-g, --grr-filename, --grr

The GRR configuration file. If the argument is absent, the a GRR repository from the current genomic context (i.e. gpf_instance) will be used or, if that fails, the default GRR configuration will be used.

--grr-directory

Local GRR directory to use as repository.

-R, --reference-genome-resource-id, --ref

The resource id for the reference genome. If the argument is absent the reference genome from the current genomic context will be used.

-G, --gene-models-resource-id, --genes

The resource is of the gene models resource. If the argument is absent the gene models from the current genomic context will be used.

-ar, --allow-repeated-attributes

Rename repeated attributes instead of raising an error.

Default: False

--verbose, -v, -V

Default: 0

--logfile

File to log output to. If not set, logs to console.