The raw data of all studies published in IDR can be downloaded using the Aspera protocol. The Aspera server is available using the following details:
Each published study has an associated passwordless username matching the IDR
accession number e.g.
Download and install the Aspera desktop client.
You must also download and configure the Aspera public key
asperaweb_id_dsa.openssh to connect to the server.
Connections to open the connection manager and add the following:
NNNNis the IDR study identifier, e.g.
Import a key from the filesystem→ select
asperaweb_id_dsa.openssh(this only needs to be done if you haven’t previously imported this key)
You should now be able to connect to the Aspera server and see the raw data for your chosen IDR study.
The Aspera command line client can be downloaded
here. The following command
will download all the raw data associated with the
$ ascp -TQ -l40m -P 33001 -i "path/to/asperaweb_id_dsa.openssh" firstname.lastname@example.org:. /tmp/data/idr0008/
Refer to the Aspera documentation for more details about the command-line options.
For convenience, a Docker image is available with the IDR download options. You can use it as follows:
$ docker run -ti --rm -v /tmp/data/idr0008:/data imagedata/download idr0008 . /data
The two examples above will download the entire content of a submission. The size of each study varies from a few GB to several tens of TB.
Sometimes it is desirable to download only a subset of the submission e.g. only one plate from a screen.
First you need to find the relative path to be downloaded. The easiest way is to use the TSV files available for all IDR studies in the curated metadata repository. For example,
After removing the leading
/uod/idr/filesets/<idrNNN>-<author>-<description>/, you can then download a
subfolder using the same commands as above:
$ ascp -TQ -l40m -P 33001 -i "path/to/asperaweb_id_dsa.openssh" email@example.com:20180215/3105/Pos0 /tmp/data/idr0040_partial
$ docker run -ti --rm -v /tmp/data/idr0040_partial:/data imagedata/download idr0040 20180215/3105/Pos0 /data
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