The https://hub.docker.com/r/imagedata/download image can be used to acquire the original files which were imported into IDR:
docker run -ti --rm -v /tmp/data:/data imagedata/download SOURCE TARGET
where SOURCE can be any subfolder under https://ftp.ebi.ac.uk/pub/databases/IDR/. For instance
docker run -ti --rm -v /tmp/data:/data imagedata/download idr0001-graml-sysgro/20151116-verified/JL_120731_S6A /data/JL_120731_S6A
Calling docker run as above envokes ascp to download the specified IDR dataset.
Note that you can modify the environment variables in the dockerfile directly in the command line.
For example, to increase the download rate to 100 Mbps, add an environment variable to the docker run command line:
docker run -ti --rm -v /tmp/data:/data -e ASCP_LIMIT=100m imagedata/download idr0001-graml-sysgro/20151116-verified/JL_120731_S6A /data/JL_120731_S6AYou can modify additional variables as well
| Variable | ASCP flag | Default | Description |
|---|---|---|---|
| ASCP_KEY | -i |
/home/data/.aspera/connect/etc/asperaweb_id_dsa.openssh | private_key_file |
| ASCP_LIMIT | -l |
40m | max_rate |
| ASCP_RETRANSFER_FILE | -k |
0 | Transfer file overwrite |
| ASCP_PORT | -P |
33001 | ssh-port |
| ASCP_USER | NA | fasp-public | user |
| ASCP_SERVER | NA | fasp.ebi.ac.uk | host |
For a more detailed description of these commands, see the ascp documentation.