Requirements (see below for installation instructions):
- Python 3.6 and pip
- Git (download Git for Windows)
- The OpenShift CLI (
occommand) is required if you want to use experimental features to run services and workflows on OpenShift
Enabling commandline autocompletion in the terminal provides a better experience using the
- ZSH: add the import autocomplete line to the
Set your terminal to use ZSH by default:chsh -s /bin/zsh
- Bash: add the import autocomplete line to the
Bash autocompletion needs to be tested.
Support of the d2s tool on Windows is a work in progress.
- Most workflow orchestrators do not support Windows, as workflows are based on Linux containers, see CWL workflows and Nextflow.
- Windows can run Docker, but not natively like Linux, making it more prone to errors.
CWL Workflow execution on Windows with the CWL reference runner works great with WSL 2 and Docker Desktop.
We recommend to use the Windows PowerShell terminal (which is easier to use than the basic terminal).
You need to open a new terminal for the autocomplete to be activated.
d2scommand in the terminal to see all the available options (it will adapt to the command and dynamically retrieve your datasets and workflows!).
For licensing reason the GraphDB RDF triplestore free edition distribution needs to be downloaded manually 📥
Go to https://ontotext.com/products/graphdb/ and provide informations to get an email with the link to download GraphDB
Download the latest version of GraphDB as stand-alone server free version (
d2sclient will ask you to provide the path to the GraphDB distribution
.zipfile when initializing the workspace.
By default the
d2sclient will try to get the file from your home directory (e.g.
/home/my-user)# Copy the GraphDB distribution file to your home foldercp graphdb-free-*-dist.zip ~/
Update GraphDB version
Change the GraphDB version used by
d2s to the one you downloaded by changing
GRAPHDB_VERSION in the file
.env in your project folder.
If you just want to run
d2s we recommend you to use pipx as it install the tool in an isolated environment. It can be compared to
Consider doing a
pip install --upgrade pipto update your pip installation.
pip3to make sure
pipxis installed with Python3, but feel free to use your own
pip3 if not installed.
- Open the PowerShell as administrator to install Chocolatey and its packages.
- Check and fix system restrictions:
- Install Chocolatey on PowerShell:
See the official Chocolatey documentation.
Chocolatey can also be installed using a non-administrative shell. See the documentation.
Open the PowerShell as administrator and use Chocolatey to install Python 3.8 and pip:
A reboot of your system is required to complete the installation.
Pip does not need to be run as administrator (only
Upgrade d2s to the latest release:
If you face issues where
cwl-runner is already installed, try to make sure it is properly uninstall from
If you are facing issue with
No module name pip found, it might be due to pip and pipx version issues. Be careful when installing
pipx as you want it to properly use
python3.6. Those commands will help you uninstalling
sudo groupadd dockercould be required before
usermodif the group has not been created.
Use the Docker installer for MacOS (
.dmg file) to install Docker and
You can change Docker settings by clicking on the Docker icon 🐳 in the top bar, then click Preferences...
/tmp should be shared by default. It is recommended to create the
d2s project folder in a subfolder of
If you have Windows home or don't want to create a DockerHub account, use docker-toolbox:
Docker Quickstart Terminal to start Docker.
Additional components that might be needed to install (VM and GUI):choco install virtualbox docker-kitematic
Virtualization and Hyper-V must be activated. Check in the
Task Manager , in tab
Performance if Virtualization is
Check the documentation to enable it.
Docker-desktop installation will propose to install virtualization automatically after the Docker installation, if they are not installed.
Note that Docker Hyper-V is not available for Windows 10 Home edition (you will need Pro or Enterprise edition)
You might need to access the BIOS to enable VT-x virtualization
docker-toolbox are sharing your
C:/Users volume. Docker will only be able to access folders and files in the
Shared Drives. So make sure you execute
d2s init somewhere in your users directories.
docker-desktopyou can change it in Docker config >
Shared Drives> Share Drive C
docker-toolboxyou need to change the settings of the Virtual Box
DNS issue: Docker build can't access the internet. E.g.: getting
wget: unable to resolve host address
If Docker can't access internet when building you might want to change the DNS (to use Google's one).
On Linux:nano /etc/resolv.conf> nameserver 22.214.171.124
On Windows: go to
Firewall issue on Windows: it is common to face a firewall when Docker tries to connect to the internet
- This could be due to local services: try deactivate your firewall and/or antivirus
- If you are running it on your office network you might face issues related to the office network firewall. Try at home and contact your IT department if needed.
For more details on how to run Docker see the Docker guide.
Rabix Benten is a plugin for completion, error and warning messages for CWL files in Visual Studio Code.
Install the package using
CWL (Rabix/Benten) extension to Visual Studio Code.
Rabix Composer is a nice way to visualize CWL workflows.
Download the right installation file and run it.
d2s-corefolder in Rabix Composer.
Note that Rabix will overwrite how you originally wrote your CWL files, and add
xycoordinates to steps.
Apache Airflow allow to run and monitor workflows. It requires to install the
cwl-airflow package to add CWL compatibility.
FileNotFoundError:[Errno 2]No such file or directory:'airflow'
Submit a workflow:
To be tested.
Toil is a Python workflow manager which allows to run CWL workflows.
Install Toil for CWL:
Run a workflow
To be tested.