Getting Started

Core facility website: http://bioinformatics.danforthcenter.org/

Cluster status: http://bioinformatics.danforthcenter.org/ganglia/?c=Bioinformatics

Documentation: http://bioinformatics.readthedocs.io/

GitHub: https://github.com/danforthcenter/

Docker: https://hub.docker.com/u/danforthcenter/

Slack (virtual help desk): https://ddpsc-bioinfo.slack.com

Jupyter Notebook server: https://jupyter.ddpsc.org

Login (SSH/SFTP) server: apollo.ddpsc.org

Globus GridFTP server: chronos.bioinformatics.danforthcenter.org (see here for more details)

Setting up your workstation

Jupyter Notebook access

On any platform, point your web browser to https://jupyter.ddpsc.org and enter your Bioinformatics username and password.

Command-line access

Applications

You will need a terminal application that supports ssh to log into the Bioinformatics infrastructure. Below are some recommended applications by platform.

Mac OSX: Terminal (built-in), iTerm2

Linux/Unix: Terminal (built-in)

Windows: Windows Subsystem for Linux (Windows 10 only), PuTTY, Cygwin

Logging in

To log into the system via ssh, open one of the above applications and enter the command:

ssh username@apollo.ddpsc.org

where username is your Bioinformatics username. The first time you log in you will need to type "yes" to accept the server's key.

File access

Applications

Mac OSX: Cyberduck/Mountain Duck, Transmit, FileZilla

Linux/Unix: System file browser (built-in, )FileZilla

Windows: Cyberduck/Mountain Duck, WinSCP, FileZilla

The above applications will let you quickly browse the Bioinformatics filesystem. Many will even let you edit files directly on the server from your local computer.

For large file transfers it is often better to download directly from the source onto the system without using your local computer as a mid-point stop. This can be done on the server chronos or in the HTCondor cluster using wget or curl.

You can also Globus GridFTP to transfer files between your computer or other remote endpoints and the Bioinformatics endpoint. See our Globus guide for more information.

Running jobs

See our HTCondor guide for more information.