Command Line Interface#
modo#
Multi-Omics Digital Objects command line interface.
modo [OPTIONS] COMMAND [ARGS]...
Options
- --endpoint <endpoint>#
URL of modos server.
- --version#
Print version of modos client
Environment variables
- MODOS_ENDPOINT
Provide a default for
--endpoint
add#
Add elements to a modo.
modo add [OPTIONS] OBJECT_PATH ELEMENT_TYPE:{sample|assay|data|reference}
Options
- -p, --parent <parent>#
Parent object in the zarr store.
- -e, --element <element>#
Create instance from element metadata provided as a json string.
- -f, --from-file <from_file>#
Include a data file associated with the instance. The file must be in json or yaml format.
- -s, --source-file <source_file>#
Specify a data file (if any) to copy into the digital object and associate with the instance.
Arguments
- OBJECT_PATH#
Required argument
Path to the digital object. Remote paths should have format s3://bucket/path
- ELEMENT_TYPE#
Required argument
Type of element to add to the digital object.
create#
Create a modo interactively or from a file.
modo create [OPTIONS] OBJECT_PATH
Options
- -f, --from-file <from_file>#
Create a modo from a file. The file must be in json or yaml format.
- -m, --meta <meta>#
Create instance from metadata provided as a json string.
Arguments
- OBJECT_PATH#
Required argument
Path to the digital object. Remote paths should have format s3://bucket/path
list#
List remote modos on the endpoint.
modo list [OPTIONS]
publish#
Export a modo as linked data. Turns all paths into URIs.
modo publish [OPTIONS] OBJECT_PATH
Options
- --output-format <output_format>#
- Default:
RdfFormat.TURTLE- Options:
turtle | xml | json-ld
- --base-uri <base_uri>#
Arguments
- OBJECT_PATH#
Required argument
Path to the digital object. Remote paths should have format s3://bucket/path
remove#
Removes an element and its files from the modo.
modo remove [OPTIONS] OBJECT_PATH [ELEMENT_ID]
Options
- -f, --force#
Skip confirmation for file deletion and allow deletion of the root object.
- Default:
False
Arguments
- OBJECT_PATH#
Required argument
Path to the digital object. Remote paths should have format s3://bucket/path
- ELEMENT_ID#
Optional argument
The identifier within the modo. Use modos show to check it. Leave empty to remove the whole object.
search-codes#
Search for terminology codes using free text.
modo search-codes [OPTIONS] SLOT
Options
- -q, --query <query>#
Predefined text to use when search codes.
- -t, --top <top>#
Show at most N codes when using a prefedined query.
- Default:
50
Arguments
- SLOT#
Required argument
The slot to search for codes. Possible values are cell_type, source_material, taxon_id
show#
Show the contents of a modo.
modo show [OPTIONS] OBJECT_PATH [ELEMENT_ID]
Options
- -z, --zarr#
Show the structure of the zarr archive
- Default:
False
- -f, --files#
Show data files in the digital object.
- Default:
False
Arguments
- OBJECT_PATH#
Required argument
Path to the digital object. Remote paths should have format s3://bucket/path
- ELEMENT_ID#
Optional argument
The identifier within the modo. Use modos show to check it.
stream#
Stream genomic file from a remote modo into stdout.
modo stream [OPTIONS] FILE_PATH
Options
- -r, --region <region>#
Restrict stream to genomic region (chr:start-end).
Arguments
- FILE_PATH#
Required argument
The s3 path of the file to stream . Use modos show –files to check it.
update#
Update a modo based on a yaml file.
modo update [OPTIONS] OBJECT_PATH
Options
- -c, --config <config_file>#
Required File defining the updated modo. The file must be in json or yaml format.
- -n, --no-remove#
Do not remove elements that are missing in the config_file.
- Default:
False
Arguments
- OBJECT_PATH#
Required argument
Path to the digital object. Remote paths should have format s3://bucket/path