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.
For queries regarding UPPMAX servers, please contact support@uppmax.uu.se
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.
Please see this link.
There is a dds module installed on Rackham. To load it, please enter:
module load bioinfo-tools
module load dds-cli
dds
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.
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.
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:
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
.
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.
Type:
dds user info
Simply enter:
dds project status display -p <deliveryproject>
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
.
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
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.
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.
Note that only PI’s/project owners can invite members. For instructions please see: https://scilifelabdatacentre.github.io/dds_cli/examples/#user-examples.
Contact the bioinformatician who sent you the delivery e-mail or support@ngisweden.se.
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.
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.
Please visit this link: https://delivery.scilifelab.se/reset_password.
Last Updated: 17th January 2023