Data delivery DDS

How to receive your data

When a project is ready for delivery, NGI registers a new delivery project with DDS.
DDS (Data Delivery System) is a command-line tool developed by the Data Centre at SciLifeLab together with NGI. It consists of a command-line-interface (CLI) and a web interface. Data uploaded to DDS is securely encrypted at all times and can only be decrypted by members of the specific project.

Initially, the PI of the sequencing or genotyping project will be assigned as the PI of the delivery project in DDS. The bioinformatics responsible person specified on the order will be added as a member of the delivery project. When the delivery project has been created, the PI and any member of the project will receive an e-mail from SciLifeLab saying that the project is now available for access.
The PI can administer the delivery project and, can therefore, add or remove member(s) and set members as project owners through the DDS CLI .
Members of the delivery project are able to download the data or have the data copied to Bianca (for more information about how DDS works for Bianca, please see this link.)
After delivery with DDS, the PI is solely responsible for ensuring the integrity, availability and safekeeping of the sequencing or genotyping data and associated files, as well as ensuring that the data is handled in accordance with applicable legislation.

Delivery projects are only active for 45 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 DDS.

Planning for Sequencing Data Storage and Access

Sequencing projects can generate data volumes ranging from a few gigabytes to several hundred gigabytes per sample, quickly adding up to more than the storage capacity of a standard computer. As a result, it is important to plan ahead to have a solution in place for storing and working with the data before it is delivered. This could be your local university or institutions storage system, a cloud service, or another infrastructure that suits your needs. If you do not already have access to suitable resources one option is to apply for a project allocation through NAISS, the Swedish national infrastructure for computing and storage. NAISS provides resources for academic researchers that can be used for storing sequencing data and performing analysis. NAISS allocation proposals are reviewed either continuously or during specific call periods, depending on the type of project request. Because the process can take time, we recommend starting your application well in advance of when you expect your data to be delivered. You can read more and apply at https://www.naiss.se/allocations/ If you have questions or need help preparing for your data delivery you are welcome to contact us.

For queries regarding UPPMAX servers, please contact support@uppmax.uu.se

Getting started

A DDS account is needed to access your data. An e-mail with registration instructions will be sent to you from services-noreply@scilifelab.se when you are added to your first project in DDS. Please note that you need to register within one week after you have received the e-mail. Subsequently, you can use this account to access further projects, if applicable.

Running DDS on Bianca

Please see this link.

Running DDS on Rackham

There is a dds module installed on Rackham. To load it, please enter:

module load bioinfo-tools
module load dds-cli
dds

Running DDS on your own server

Please visit this link to find executables for MacOS, Linux, and Windows as well as installation instructions.
If you prefer to install DDS without the executables, please see this link.

Logging in

To verify that DDS has been installed you can type dds to see the help commands.

To log in, type:

dds auth login

Here you add the username and password that you created when you received the registration e-mail. You will shortly receive an e-mail with a one-time authentication code (sent from services-noreply@scilifelab.se).
However, please note that it has been observed that some e-mail servers have a special spam filter, which may affect the time it takes for the e-mail to arrive. Finally enter the token code to log in. To log out enter dds auth logout. Please note that you will receive a new token code (sent to your e-mail) every time you log in. If you don’t log out, your session will be valid for one week.

Listing projects

To see a list of the projects of which you are a member of, enter:

dds ls

In this table you can also see who the PI of the project is, which status the project has, when it has been last updated, and the size. The status will be one of the following:

“In progress”: the project is open but the data is not yet available for download

“Available”: the data is available for download

“Archived”: the project has been closed due to project having reached its expiration date (45 days after the date of delivery)

The command prompt will ask you if you want to view the files. To download specific files this step is necessary (to see the file names of the projects), but if you wish to just download all files of a project or just view the list you can exit by pressing enter.

To see the project content, fill in project name when the prompt asks (Project ID:), followed by enter. This will display a folder or file tree structure. You could also type:

dds ls -p <deliveryproject> --tree

Remember you can always see the listing options in dds ls --help.

Downloading data

To download data of a project you use the command dds data get. To see a list of options, type:

dds data get --help

The asterisk shows you which option is required, all other options are optional. It is recommended to verify the integrity of the download using --verify-checksum.

Before you download please make sure you have enough disk space. To see the size of individual folders and files enter:

dds ls -p <deliveryproject> --size

To download all content of a project into a destination path, enter:

dds data get -p <deliveryproject> -a --verify-checksum -d <destinationpath>

The “a” stands for “all” content and the “d” for destination path.

You can see if the verification went OK if it says “Checksum verification successful. File integrity verified”. If this does not get displayed or you get a message saying something similar to “Checksum verification failed. File compromised.”, please try to download the files one more time. If the problem remains, please contact the bioinformatician who delivered the data.

Other commands

Viewing information about your account

Type:

dds user info

Viewing the status and deadline of a project

Simply enter:

dds project status display -p <deliveryproject>

Data must be retrieved before the delivery project expires, which happens 45 days after delivery, unless agreed otherwise. It is the responsibility of the PI for the delivery project to ensure that data is retrieved.

Adding users to projects

To add a new user to a project you need to be (set as) the project owner of a project (usually the PI). Type:

dds user add <emailaddress> -p <deliveryproject> -r role

Where “emailaddress” is the members e-mail address. The role of the new member to add can either be “Researcher” or “Project Owner.” To see the options of adding users please enter dds user add --help.

Deleting your account

You can request having your own account deleted (you will lose access to any projects that you currently belong to).

Type (warning, cannot be undone!):

dds user delete --self

Using the web interface

The web interface is found at https://delivery.scilifelab.se/.

For now, the web interface can only be used to register, list projects, change and reset passwords.

Video tutorials

Frequently asked questions

I have not received an e-mail to register for DDS

Some mail servers have a spam filter delaying the e-mail, but if there have been more than 24 hours since you received the delivery e-mail by NGI, please contact the bioinformatician who sent the delivery e-mail or support@ngisweden.se.

Please note that you will only receive the e-mail to register for DDS once, the first time you are added to a project. The following e-mails will only contain information about which DDS projects you are added to.

How can I add a member to a DDS project?

Note that only PI’s/project owners can invite members. For instructions please see: https://scilifelabdatacentre.github.io/dds_cli/examples/#user-examples.

I’m supposed to have access to a DDS project, but I don’t, how do I get access?

Contact the bioinformatician who sent you the delivery e-mail or support@ngisweden.se.

When I log in to DDS it says that a project is ”in progress”, what does this mean?

It means that a DDS project has been created, but it has not yet been made available, most often because the data upload has not finished yet. If the project is still set as ”in progress” several hours after you have received the delivery e-mail by NGI, please contact the bioinformatician who sent you the delivery e-mail or support@ngisweden.se.

I did not register to DDS within one week, how do I gain access?

Please note that you need to register within one week after you have received the e-mail or the link will not be valid.
Contact the bioinformatician who sent you the delivery e-mail or support@ngisweden.se.

I have forgotten my DDS password, how do I reset it?

Please visit this link: https://delivery.scilifelab.se/reset_password.

Last Updated: 12th August 2025