Note The EBI Cloud Portal has been retired and its code base is no longer updated. This includes all tooling for the VM-related features of the BioExcel Portal.
If you would like to contact the Cloud Portal authors, please leave us feedback via the EBI contact form mentioning the EBI Cloud Portal in the Subject.
As of March 2023 the BioExcel project itself is ongoing and you can find more information on its official website.
Cloud Portal application to create VM and install jupyter server on it. It uses the ubuntu 18.04-python image from openstack and installs conda, jupyter using ansible.
Import project to ECP, enter inputs if required and deploy.
| Parameter name (default) | Example value | Description |
|---|---|---|
remote_user (ubuntu) |
||
machine_type (s1.small) |
Flavour of the instance | |
floating_ip_pool (ext-net) |
Preexisting Floating IP pool | |
network_name |
PROJECT-network |
Preexisting network to which an instance will be attached |
repo_url |
https://github.com/bioexcel/biobb_wf_md_setup |
URL of Github repository containing the notebook |
conda_environment |
biobb_MDsetup_tutorial |
Conda Environment name |
conda_environment_file_path |
conda_env/environment.yml |
Conda environment file path relative to the repository root |
python_version |
3.6 |
Python version for Conda Environment |
package_install |
conda install pocl; conda install -y -c bioconda biobb_analysis==2.0.1 |
Specify additional install commands, separated with a semicolon (;). Arbitrary list of packages will be installed, when environment path not specified plus pocl, when package_install not specified |
post_install |
jupyter-nbextension enable --py --user widgetsnbextension; jupyter-nbextension enable --py --user nglview |
Specify some additional commands to execute after activating environment. Arbitrary jupyter-nbextension command executed, when package_install not specified |
docker_install |
yes or no |
the flag to set whether docker needs to be installed or not |
| Parameter name | Parameter value |
|---|---|
disk_image_name |
ubuntu-18.04-python |
The virtual machine provided will have this ports open.
ICMP: all
TCP : 22
TCP : 8443