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.
- --debug#
Enable debug logging.
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>#
Read instance metadata from a file. 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.
c4gh#
Local encryption via crypt4gh.
modo c4gh [OPTIONS] COMMAND [ARGS]...
decrypt#
Decrypt a local MODO.
modo c4gh decrypt [OPTIONS] OBJECT_PATH
Options
- -s, --secret-key <secret_key>#
Required Secret key of the recipient to decrypt files in the MODO.
- -pw, --passphrase <passphrase>#
Path to file with passphrase to unlock secret key.
Arguments
- OBJECT_PATH#
Required argument
Path to the digital object. Remote paths should have format s3://bucket/path
encrypt#
Encrypt a local MODO.
modo c4gh encrypt [OPTIONS] OBJECT_PATH
Options
- -p, --public-key <public_key>#
Required Public key(s) of the recipent(s) to decrypt files in the MODO.
- -s, --secret-key <secret_key>#
Secret key of the sender to encrypt files in the MODO.
- -pw, --passphrase <passphrase>#
Path to file with passphrase to unlock secret key.
Arguments
- OBJECT_PATH#
Required argument
Path to the digital object. Remote paths should have format s3://bucket/path
codes#
Terminology codes utilities.
modo codes [OPTIONS] COMMAND [ARGS]...
search#
Search for terminology codes using free text.
modo codes search [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
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
enrich#
Enrich metadata of a digital object using file contents.
modo enrich [OPTIONS] OBJECT_PATH
Arguments
- OBJECT_PATH#
Required argument
Path to the digital object. Remote paths should have format s3://bucket/path
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
remote#
Remote object management.
modo remote [OPTIONS] COMMAND [ARGS]...
download#
Download a modo from a remote endpoint.
modo remote download [OPTIONS] OBJECT_PATH
Options
- -t, --target <target_path>#
Required Path where to download the digital object.
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 remote list [OPTIONS]
stream#
Stream genomic file from a remote modo into stdout.
modo remote 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.
upload#
Upload a local modo to a remote endpoint.
modo remote upload [OPTIONS] OBJECT_PATH
Options
- -t, --target <target_path>#
Required S3 path where to upload the digital object (format: s3://bucket/name).
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.
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.
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.
- -f, --force#
Force deletion of 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