Customization¶
Currently we offer the following ways of customizing your virtual machine at startup
- Conda packages
- Research environments
Conda¶
From the project page:
Conda is an open-source package management system and environment management system that runs on Windows, macOS, and Linux. Conda quickly installs, runs, and updates packages and their dependencies. Conda easily creates, saves, loads, and switches between environments on your local computer. It was created for Python programs but it can package and distribute software for any language.
Responsibility
All Conda tools are created, provided and maintained by third parties. The de.NBI cloud is not responsible for the functionality of the packages provided. In case of problems during installation or use, please contact the developers of the respective packages.
You may choose from a list of Bioconda, Anaconda and Condaforge tools. You may filter for name, version und build version
to find the tools you need.
Click on the green plus sign to add the tool or click on the red minus sign to remove the tool from your selection of tools.
When you are happy with your selection, we need your confirmation about the install process which will proceed.
Installation process¶
Minoconda3
Miniconda3 will be installed, which is a lightweight package manager, not the full (~1500 package) Anaconda set of tools. If you wish to install Anaconda, you will have to choose it from the list of packages.
We will create a temporary private and public key pair which will be used to access your virtual machine at startup.
Then we will install your selection with Ansible.
At the end of the installation process we will remove the temporary key from your machine and copy your public key onto it,
regardless of whether the installation of your selection will succeed or fail.
Also you will be able to download the installation logs (as pdf or txt file) and look into the them if you wish
here.
Environment¶
A Conda environment named 'denbi' will be created. You may find your selection of tools in this environment. For your convenience, we initialize the .bashrc for conda and create an alias, so that you may load the 'denbi' environment simply by running
$ denbi
Research environments¶
Here you may find a selection of research environments you will be able to use over your web browser, e.g.
JupyterLab, RStudio, Apache Guacamole or Theia IDE. More research environments might
be added in the future.
You will need to select a template of the research environment you wish to install and a namespace, which will be part
of the URL under which you will have access to your research environment.
You may also choose the No install option if you already installed a research environment (e.g. when starting
a new instance from a previous snapshot). This option will only take the necessary steps for access.
Installation
Similiar to the installation process of Conda, we will create a temporary rsa-keypair which will be used to install your research environment via Ansible. Afterwards we remove the temporary key and copy your public key onto your virtual machine, whether the process succeeds or fails. Afterwards you may download and look into the installation logs if you wish to.
Where to find the URL¶
To access your research environment, follow the Link you will find on the instance overview
and/or on the detail page of your virtual machine.
If you are not already logged in with your LifeScience account, you will be prompted to log in with your LifeScience account, as only the one who started the virtual machine will be allowed to access the research environment.
JupyterLab¶
From the project page:
JupyterLab is the latest web-based interactive development environment for notebooks, code, and data. Its flexible interface allows users to configure and arrange workflows in data science, scientific computing, computational journalism, and machine learning. A modular design invites extensions to expand and enrich functionality.
To access your JupyterLab research environment, please follow the link you may find after starting your virtual machine, in the instance overview and/or on the detail page of your virtual machine. You will be prompted to log in with your LifeScience account if you have not done it already. Afterwards you will be prompted to log in to JupyterLab with a Token.
Login Token¶
Use the following Token:
simplevm
Now you are able to work with JupyterLab via web browser!
RStudio¶
From the project page:
RStudio is an integrated development environment (IDE) for R. It includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management.
To access your RStudio research environment, please follow the link you may find after starting your virtual machine,
in the instance overview and/or on the detail page of your virtual machine. You will be prompted to log in with your
LifeScience account if you have not done it already. Afterwards you will be prompted to log in to RStudio.
Login credentials¶
Use the following credentials:
Username: ubuntu
Password: simplevm
Username: ubuntu
Password: ogvkyf
Multiple users and concurrent sessions¶
If you want to allow other users access to your research environment, you need to add them to the allowed list of users which you may find at the detail page. Please note that this does not automatically allow for concurrent sessions, which means that your session will be terminated once another allowed user logs in with the same credentials. To allow for concurrent sessions, please refer to this guide.
Apache Guacamole¶
From the project page:
Apache Guacamole is a clientless remote desktop gateway. It supports standard protocols like VNC, RDP, and SSH. We call it clientless because no plugins or client software are required. Thanks to HTML5, once Guacamole is installed on a server, all you need to access your desktops is a web browser.
Info
After rebooting or turning from shutoff to active, it will take about 15 minutes until you are able to access your Apache Guacamole research environment.
To access your Apache Guacamole research environment, please follow the link you may find after starting your virtual
machine, in the instance overview and/or on the detail page of your virtual machine. You will be prompted to log in
with your LifeScience account if you have not done it already. Afterwards you will be prompted to log in to Apache Guacamole.
Login credentials¶
Use the following credentials:
Username: denbi
Password: denbi
It may happen that in case of inactivity the password for the ubuntu user is requested which is:
ogvkyf
Multiple users and concurrent sessions¶
If you want to allow other users access to your research environment, you need to add them to the allowed list of users which you may find at the detail page. Please note that this does not automatically allow for concurrent sessions, which means that your session will be terminated once another allowed user logs in with the same credentials. To allow for concurrent sessions, please refer to this guide.
Theia IDE¶
From the project page:
Eclipse Theia is an extensible platform to develop full-fledged multi-language Cloud & Desktop IDE-like products with state-of-the-art web technologies.
More information regarding Theia IDE can be found on our tutorial page.
To access your Apache Guacamole research environment, please follow the link you may find after starting your virtual
machine, in the instance overview and/or on the detail page of your virtual machine. You will be prompted to log in with
your LifeScience account if you have not done it already. Now you are able to work with Theia IDE via web browser!
