When a project is ready for delivery, NGI registers a new delivery project with the Swedish National Infrastructure for Computing (SNIC). Data is delivered via resource called “GRUS” hosted by SNIC-UPPMAX.
Delivery projects are only active for 90 days after data delivery and will expire thereafter. The PI of the delivery project is responsible for ensuring that data is retrieved before the delivery expires. Once the delivery has expired, it is automatically removed from GRUS.
For queries about retrieving data from from GRUS or queries regarding UPPMAX servers, please contact firstname.lastname@example.org
This is a condensed version of the GRUS user guide provided by UPPMAX. If you find the instructions below too brief, please refer to that guide or please watch the tutorial videos at the NGI YouTube channel.
Typical deliveries from NGI consist of large amounts of data and we generally don’t recommend using a graphical software for downloading. We recommend using a command line client for SFTP transfers. Many different clients are freely available, such as tools from OpenSSH for e.g. Linux and MacOSX or Putty for Microsoft systems. In the examples below, we use the sftp client, which comes bundled with most Linux distributions.
Note that if you are going to transfer data from GRUS to a compute project on the Bianca or Rackham HPC resources, you should use the data transfer service provided by UPPMAX, rather than transferring files over SFTP.
In order to be able to retrieve data from GRUS via SFTP, you must:
For accessing GRUS, the username is constructed from your regular UPPMAX username and the name of the delivery project to access, separated by a hyphen (‘-‘). That is, if your username is myuser and the delivery project is delivery00001, the username for GRUS will be myuser-delivery00001. Similarly, the password is your UPPMAX password followed by the current six-digit code generated by your two-factor application. That is, if your regular password is mypassword and the current two-factor code is 123456, the GRUS password is mypassword123456.
get -r . /path/to/local/destination/folder/
find /path/to/local/destination/folder/ -name "*.md5"
cd folder/containing/file_with_checksums && md5sum -c file_with_checksums.md5
You do not need to use SFTP if you plan to analyse your project data on the UPPMAX resources (Bianca and/or Rackham). UPPMAX provides a mechanism to transfer data from GRUS to your Bianca/Rackham project with minimum effort. See the Deliver user guide for details.
If you prefer to view the tutorials in Swedish, there are Swedish versions for downloading your sequencing data to an UPPMAX server here, and a video showing how to download your sequencing data to your own server here.
lftp, may be more suitable for downloading. However, because the code for two-factor authentication is used as part of the password, you cannot use features of the client that involves making additional connections to the server. Be sure to disable such behaviour.
NGI will create the delivery project. No action is required by the project members until they receive an e-mail from the NGI.
md5sum -c file_with_checksums.md5but the exact command may vary depending on the tool used and the format of the md5 checksum file. You should ensure that the verification doesn’t report any inconsistencies and that all files have been verified.
Data must be retrieved before the delivery project expires, which happens 90 days after delivery, unless agreed otherwise. It is the responsibility of the PI for the delivery project to ensure that data is retrieved.
I received an email saying that “Your SNIC project at UPPMAX is created” for a project with type “NGI Delivery”, what does this mean?
This means that NGI has started delivering data to you and you will receive further information from NGI shortly. You can also log in to the SUPR web interface and view the project details.
I’m having problems logging into GRUS or I cannot see any data when I log in, who should I contact?
Please contact the responsible bioinformatician who sent you the e-mail containing the delivery project. With more technical issues, please contact the UPPMAX support.
I have a question about the contents of the data delivery, who should I contact?
Please contact responsible project coordinator(s). Visit the Contact page.
I need to apply for compute resources, who should I contact?
For Swedish academia, SNIC provides the resources that you can apply for.