This is a virtual workshop, you can participate by reading workshop materials, watching video presentations and carrying out exercises on an assigned BioHPC Cloud server (server assignments are listed here). If you need help, please sign up for our Office Hours. The server assigned to you for hands-on exercises will be available for a limited time, see server assignment page or bottom of this page for details. Please note, the server is assigned to you for hands-on exercises, NOT heavy computing, using the server for workshop unrelated computing is not allowed and will result in assignment termination.
This workshop is designed to prepare biologists to work in the interactive Linux environment of our BioHPC Cloud servers. We will cover basics of Linux operating system, needed to operate the servers. In particular the topics will include:
- Navigating a Linux workstation: logging in and out of a Linux machine, directory structure, basic commands for dealing with files and directories
- Working with text files
- Transfer of files to and from a Linux workstation
- Basics of running applications on Linux
- Using multiple CPUs/cores: parallel applications
- Basics of shell scripting
The presented material will be illustrated by hands-on exercises hosted on dedicated workstations of the BioHPC Cloud. The workstations will be accessed using the Secure SHell (ssh) protocol. To participate in the exercises you will need to use your own laptop or desktop with an ssh client installed. MACs and Linux laptops come with native ssh clients and no extra installation is needed. For windows, the recommended ssh client is PuTTy - please install it prior to the workshop (just download the executable file http://the.earth.li/~sgtatham/putty/latest/x86/putty.exe and put it anywhere on your hard drive; double-click to launch). To be able to run Linux programs with graphical inerface displaying on your laptop, you should also install RealVNC viewer (download one appropriate for your laptop from https://www.realvnc.com/download/viewer/). To transfer files between your laptop and a Linux machine, you will need an sftp client, such as FileZilla (although MAC and Linux laptops come with native sftp clients and no extra installation is necessary, FileZilla would be helpful on these platforms as well). For detailed instructions and more information on how to access BioHPC machines, please refer to the following document: http://biohpc.cornell.edu/lab/doc/Remote_access.pdf, especially points 1 and 2.2-2.4.
This workshop is divided into paired sessions: a lecture/presentation session (Monday) followed by a hands-on session (Wednesday), allowing plenty of time for hands-on training. All sessions will be held on Zoom between 10 am and 11:30 EDT. The Zoom links will be sent in advance to all participants via e-mail.
Access to BioHPC Cloud workstations requires a BioHPC Cloud account. If you did not already have such account, you were asked to create one at the time you registered for the workshop. It you need to re-set your BioHPC password, you can do it at https://biohpc.cornell.edu//lab/labpassreset.aspx. If you do not know your BioHPC user ID, contact us at support@biohpc.cornell.edu.
Since the BioHPC resources are behind the Cornell firewall, the easiest way to access them is from Ithaca campus network (not possible at present) or from any other location while using the Cornell VPN. The latter is avaliable to all users having the Cornell NetID. Please check the relevant CIT website to see if you are elligible for a NetID and obtain one if possible. While out-of-campus access to BioHPC Cloud without the VPN is still possible, it is somewhat more complicated.
A Linux machine for hands-on exercises will be assigned to you automatically (you do not have to make your own reservation).
Lecture slides for Part 1&2
Lecture slides for Part 3
Exercise handouts: Part 1 PDF Part 1 HTML Part 2 PDF Part 2 HML Part 3 PDF Part 3 HTML
* For Part 2, "Exercise 2: batch download of files from sequencing facility", you can get the "download.sh" file from "/shared_data/Linux_workshop/download.sh"
Workshop presentation 1
Workshop presentation 2
Workshop presentation 3
Workshop presentation 4
Workshop presentation 5
Workshop presentation 6
Workshop server assignment