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. There is a DDS documentation page by the Data Centre here. 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 email@example.com
In order to access your data you first need a DDS account. You will receive an e-mail with registration instructions when you are added to a project, either by NGI or a project owner (e.g. the PI). This e-mail will be sent from firstname.lastname@example.org. Please note that you need to register within one week after you have received the e-mail.
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
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 email@example.com).
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 this 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:
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
Before you download please make sure you have enough disk space. To see the size of individual folders and files enter:
dds ls -p
To download all content of a project into destinationpath, 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 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 firstname.lastname@example.org.
dds user info
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