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A workshop at Tulane University - May 14/16 2024
Tidewater building Room 1204
10am-12pm (pre-workshop assistance 9am-10am)
The command line is fundamental for all programming languages (e.g., R, Python), and essential for operating numerous programs that are of interest to the research community. As such, understanding its functionality opens avenues for diverse program usage, reproducible science, and remote access to high-performance computing. This 2h workshop is a a hands-on introduction to the UNIX command line, with examples of application and practice using Tulane's Cypress compute cluster.
This workshop is designed for those with little/no prior experience, but may also be of interest to those using Cypress for the first time.
Workshop goals:
- Promote open reproducible science through skills training
- Basic working understanding what command line is and what to use it for
- Demonstrate using remote hpc resources - in advance of more detailed Cypress and LONI workshops
- The Cypress wiki contains a wealth of information about the resource, including simple instructions on getting an account.
Workshop Intro Slides here
Workshop Tutorial Document here
Useful links from the tutorial:
- A very nice cheatsheet from Boyce Thompson Institute (BTI)
- Online source for info on each shell command https://explainshell.com/
The files in this repo include:
- Input sequence data
- Output alignment and tree files
- Example batch submission script for Cypress
- Example notes on retrieving sequences from NCBI
Check out other online learning resources aggregated in this list from Northwestern University: https://nuitrcs.github.io/commandlineworkshop/
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If you run into this common error: Unable to negotiate with xx.xx.xx.xx port 22: no matching host key type found. Their offer: ssh-rsa,ssh-dss