MacOS / Linux¶
You can either install the DDS CLI using pip (https://pypi.org/project/dds-cli/) or with an executable.
To perform these steps you need to have Python version 3.7 or higher installed.
To install Python, please first run
It’s possible that this shows
Python 2.7, in which case you should run
If this does not return
Python 3.7.xor higher, you will need to install Python.
Make sure you have the latest version of pip.
python3 -m pip install --upgrade pip
The DDS CLI is available on PyPi. To install the DDS CLI, open the terminal and run
$ pip install dds-cli
Once the installation has finished, test that the CLI has been installed correctly by verifying the version:
$ dds --version
This should display something like this
Data Delivery System, version 1.0.0
If the version does not say the same as what is displayed on PyPi, run the following command and try again.
$ pip install --upgrade dds-cli
Download the executable from the GitHub release page: https://github.com/ScilifelabDataCentre/dds_cli/releases/latest/download/dds_cli_macos_x86_64 If you have an M1 Mac, you need to download this one instead: https://github.com/ScilifelabDataCentre/dds_cli/releases/latest/download/dds_cli_macos_arm64
Open the terminal and go to the directory where the downloaded file is located
You should now be able to run the dds with the following command
$ ./<name-of-file> Example: $ ./dds_cli_macos_x86_64
To specify options, follow the documentation instructions. The only difference should be that you may need to change the permissions regarding executables, allowing your laptop to trust the software and finally running the dds by specifying the executables name instead of
Detailed instructions on how install the DDS CLI on Windows here.
Download the executable from the GitHub release page: https://github.com/ScilifelabDataCentre/dds_cli/releases/latest/download/dds_cli_win_x86_64.exe
Open the Powershell (Start -> Search “Powershell” -> Click) or terminal (Powershell recommended)
Drag the executable into the Powershell window and press enter. This should result in the help text being displayed.
To run the dds command, press the up arrow and use the options that you want, specified in this documentation. The only difference should be that you run the dds by specifying the executables name (/path) instead of
dds. You may need to change the permissions regarding executables and allow your laptop to trust the software.
Do not deliver sensitive data to Rackham.
The DDS CLI will be made a global module at Uppmax and you will be able to load it after having ssh:ed into Rackham. Until it is a module though, you can install the CLI with PyPi as in the previous sections.
$ pip install dds-cli
A detailed user guide for Rackham can be found here: https://www.uppmax.uu.se/support/user-guides/rackham-user-guide/
To be aware of
Mount the correct SENS project on transit
You need to have enough space on the nobackup storage allocation in the corresponding SENS project. If the data you are trying to download is larger than the allocated space, the download will fail.
If your data is larger than a few hundreds of GB: start the download in a screen/tmux session
ssh into transit
$ ssh -A <username>-<projid>@bianca.uppmax.uu.se
You will get into the home directory.
Any files that are created here are not persistent; If you download data from DDS to this directory, your data will be deleted as soon as you exit the session.
Mount your specific SENS project directory on transit
username@transit:~$ mount_wharf <sens_project>
Download the data with the DDS CLI
You must use the
--destinationoption. If you do not, the data will end up in your home directory and will be deleted when your ssh session ends.$ dds data get --destination <sens_project>/<destination>/
The downloaded data ends up in a non-backed up storage on Bianca.