Dec 16, 2016
9:00am - 4:30pm
Instructors: Saira Kazmi, Sandeep Namburi, Shane Sanders
Helpers: Joshy George, Asli Uyar
Software Carpentry's mission is to help scientists and engineers get more research done in less time and with less pain by teaching them basic lab skills for scientific computing. This hands-on workshop will cover basic concepts and tools, including program design, version control, data management, and task automation. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.
For more information on what we teach and why, please see our paper "Best Practices for Scientific Computing".
Who: The course is aimed at graduate students and other researchers. You don't need to have any previous knowledge of the tools that will be presented at the workshop.
Where: Holt Conference Room, 10 Discovery Drive, Farmington, CT 06032. Get directions with OpenStreetMap or Google Maps.
Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below). They are also required to abide by Software Carpentry's Code of Conduct.
Accessibility: We are committed to making this workshop accessible to everybody. The workshop organisers have checked that:
Materials will be provided in advance of the workshop and large-print handouts are available if needed by notifying the organizers in advance. If we can help making learning easier for you (e.g. sign-language interpreters, lactation facilities) please get in touch and we will attempt to provide them.
Contact: Please email saira.kazmi@jax.org , sandeep.namburi@jax.org or shane.sanders@jax.org for more information.
Download data from : shell-novice-data.zip
| 09:00 | Introduction to shell |
| 9:30 | Working with files and directories |
| 10:00 | Pipes, filters, sorting, saving to files |
| 10:30 | 15 minute break |
| 10:45 | Using loops for repetitive tasks |
| 11:15 | Writing Shell Scripts |
| 12:00 | 1 hour break |
| 1:00 | Finding things |
| 1:30 | Automating a Workflow |
| 2:30 | 15 minute break |
| Introduction to HPC clusters | |
| 2:45 | Connecting to clusters (ssh, scp) |
| 3:00 | Queues on HPC |
| 3:05 | Using installed software |
| 3:15 | Running Jobs on HPC |
| 3:30 | Job Arrays |
| 3:45 | Write jobs for scaling up computation (FastQC, Trimmomatic, Alignment) |
| 4:00 | Wrap up |
To participate in a Software Carpentry workshop, you will need access to the software described below. In addition, you will need an up-to-date web browser.
We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.
Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.
cmd and press [Enter])setx HOME "%USERPROFILE%"
SUCCESS: Specified value was saved.exit then pressing [Enter]This will provide you with both Git and Bash in the Git Bash program.
The default shell in all versions of Mac OS X is Bash, so no
need to install anything. You access Bash from the Terminal
(found in
/Applications/Utilities).
See the Git installation video tutorial
for an example on how to open the Terminal.
You may want to keep
Terminal in your dock for this workshop.
The default shell is usually Bash, but if your
machine is set up differently you can run it by opening a
terminal and typing bash. There is no need to
install anything.
When you're writing code, it's nice to have a text editor that is
optimized for writing code, with features like automatic
color-coding of key words. The default text editor on Mac OS X and
Linux is usually set to Vim, which is not famous for being
intuitive. if you accidentally find yourself stuck in it, try
typing the escape key, followed by :q! (colon, lower-case 'q',
exclamation mark), then hitting Return to return to the shell.
nano is a basic editor and the default that instructors use in the workshop. To install it, download the Software Carpentry Windows installer and double click on the file to run it. This installer requires an active internet connection.
nano is a basic editor and the default that instructors use in the workshop. See the Git installation video tutorial for an example on how to open nano. It should be pre-installed.
nano is a basic editor and the default that instructors use in the workshop. It should be pre-installed.