Note The EBI Cloud Portal has been retired and its code base is no longer updated.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 - bioexcel-jupyter

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.

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Requirements

Instructions

Import project to ECP, enter inputs if required and deploy.

Default values

Deployment parameters

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

Inputs

Parameter name	Parameter value
disk_image_name	ubuntu-18.04-python

Open Ports

The virtual machine provided will have this ports open.

ICMP: all
TCP : 22 TCP : 8443