Aspera

Overview

Aspera downloader is a program to download datasets from various data providers, for example the NCBI, that support use of the ascp fast downloader.

Version 3.3.3 is installed on the CSF.

Restrictions on use

Details of the licence, restrictions, links to licence docs etc

Set up procedure

We now recommend loading modulefiles within your jobscript so that you have a full record of how the job was run. See the example jobscript below for how to do this. Alternatively, you may load modulefiles on the login node and let the job inherit these settings.

Load one of the following modulefiles:

module load tools/bintools/aspera/3.3.3

Running the application

If you have an ssh cert / key file then it should be possible to run ascp in a batch job – no password will be requested if credentials are supplied in a file. If you do not have a credentials file you may run the command on the login node.

Serial batch job submission

Make sure you have the modulefile loaded then create a batch submission script, for example:

#!/bin/bash --login
#$ -cwd               # Job will run from the current directory
                      # NO '#$ -V line' - we load modulefiles in the jobscript

module load tools/bintools/aspera/3.3.3

# Optional: Provide path to our own KEYFILE for out data provider.
#           If NOT done, the default asperaweb_id_dsa.openssh will be used.
#           Using a keyfile will prevent ascp asking for a password - so
#           you must use a keyfile when running as a batch job!

KEYFILE=~/path/to/keyfile.ssh

ascp -i $KEYFILE -QT -L- -l 1000M ega-box-800@fasp.ega.ebi.ac.uk:. .
                                   #
                                   # Change the remote username and server address
                                   # as required by your data provider

Submit the jobscript using:

qsub scriptname

where scriptname is the name of your jobscript.

Further info

Updates

None.

Last modified on November 6, 2018 at 12:07 pm by George Leaver