copick download project
utils
Download tilt series and alignments from the CryoET Data Portal.
Plugin command — copick-utils
This command is provided by the copick-utils plugin, not copick core. Install it to make this command available:
See the plugin system guide for details.
Usage
Description
Fetches the AreTomo files (the raw tilt series plus their alignment files) for every
run in a CryoET Data Portal dataset and writes them to a local directory, laid out for
sub-tomogram averaging with py2rely. Pass the numeric portal dataset ID via --dataset;
all matching tilt series are downloaded in parallel into --output.
Options
| Option | Type | Default | Description |
|---|---|---|---|
-ds, --dataset |
text | required | Dataset ID to download from the CryoET Data Portal. |
-o, --output |
directory | required | Output directory to save the downloaded files. |
Examples
# Download a dataset's tilt series and alignments into the current directory
copick download project -ds 10000 -o .
# Download into a dedicated output directory
copick download project --dataset 10445 --output ./aretomo_inputs
See also
copick config dataportal— build a copick config from CryoET Data Portal datasets