datalad ukb-update

Synopsis

datalad ukb-update [-h] [-k PATH] [--merge] [-f] [--drop {extracted|archives}] [-d DATASET]

Description

Update an existing dataset of a UKbiobank participant

This command expects an ukb-init initialized DataLad dataset. The dataset may or may not have any downloaded content already.

Downloads are performed with the UKBFETCH tool, which is expected to be available and executable.

Options

-h, --help, --help-np

show this help message. –help-np forcefully disables the use of a pager for displaying the help message

-k PATH, --keyfile PATH

path to a file with an authentification key (ukbfetch -a …). If none is given, the configuration datalad.ukbiobank.keyfile is consulted. Constraints: value must be a string

--merge

merge any updates into the active branch. If a BIDS layout is maintained in the dataset (incoming-bids branch) it will be merged into the active branch, the incoming-native branch otherwise.

-f, --force

update the incoming branch(es), even if (re-)download did not yield changed content (can be useful when restructuring setup has changed).

--drop {extracted|archives}

Drop file content to avoid storage duplication. ‘extracted’: drop all content of files extracted from downloaded archives to yield the most compact storage at the cost of partial re-extraction when accessing archive content; ‘archives’: keep extracted content, but drop archives instead. By default no content is dropped, duplicating archive content in extracted form. Constraints: value must be one of (None, ‘extracted’, ‘archives’)

-d DATASET, --dataset DATASET

specify the dataset to perform the initialization on. Constraints: Value must be a Dataset or a valid identifier of a Dataset (e.g. a path)

Authors

datalad is developed by Michael Hanke <michael.hanke@gmail.com>.