Duke University

Center for Genomic and Computational Biology (GCB)

Jul 26-27, 2018

9:00am - 5:00pm

Instructors: Dan Leehr (GCB), Hilmar Lapp (GCB), Brook Moyers (Colorado State University)

Helpers: Chris Erdmann (The Carpentries), Devjanee Swain-Lenz (Duke)

Data Carpentry for Genomics

Duke's Center for Genomic and Computational Biology (GCB) is co-sponsoring and hosting a Data Carpentry for Genomics Workshop.

Data Carpentry develops and teaches workshops on the fundamental data skills needed to conduct research. Its target audience is researchers who have little to no prior computational experience, and its lessons are domain specific, building on learners' existing knowledge to enable them to quickly apply skills learned to their own research. 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 "Good Enough Practices for Scientific Computing".

Who: The course is aimed at Duke University graduate students, postdocs, faculty, and other researchers who are or will soon be working with genomics data, and who seek to acquire basic skills and confidence for doing so. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: FFSC #4233, 124 Science Drive, Durham, NC 27708. Get directions with OpenStreetMap or Google Maps.

When: Jul 26-27, 2018. Add to your Google Calendar.

Tuition & Registration: Tuition is $100.00, and is waived for graduate students except for no-shows. Therefore, you need to provide a fund code as part of registration. To register, please fill out and submit this online form. Attendance is capped at 25 learners. When the cap is reached, registrants will be put on a waitlist. To cancel your registration, you must notify us at least 3 business days prior to the workshop, or you will be charged full tuition.

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. Instructions about specific software packages to be installed prior to the workshop will be posted here about 3 weeks in advance. Participants are also required to abide by Data Carpentry's Code of Conduct.

Accessibility: We are committed to making this workshop accessible to everybody. The workshop organizers have checked that:

Contact: Please email hilmar.lapp@duke.edu for more information.


Surveys

Please be sure to complete these surveys before and after the workshop.

Pre-workshop Survey

Post-workshop Survey


Schedule

This workshop follows the Data Carpentry for Genomics curriculum.

July 26 (Day 1)

Before starting Pre-workshop survey
Morning Project organization and management
AfternoonIntroduction to the command line
Evening END

Syllabus

See lesson links under the Data Carpentry Genomics curriculum.


Setup

To participate in a Data 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.

The Bash Shell

Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.

Windows

Video Tutorial
  1. Download the Git for Windows installer.
  2. Run the installer and follow the steps bellow:
    1. Click on "Next".
    2. Click on "Next".
    3. Keep "Use Git from the Windows Command Prompt" selected and click on "Next". If you forgot to do this programs that you need for the workshop will not work properly. If this happens rerun the installer and select the appropriate option.
    4. Click on "Next".
    5. Keep "Checkout Windows-style, commit Unix-style line endings" selected and click on "Next".
    6. Keep "Use Windows' default console window" selected and click on "Next".
    7. Click on "Install".
    8. Click on "Finish".
  3. If your "HOME" environment variable is not set (or you don't know what this is):
    1. Open command prompt (Open Start Menu then type cmd and press [Enter])
    2. Type the following line into the command prompt window exactly as shown:

      setx HOME "%USERPROFILE%"

    3. Press [Enter], you should see SUCCESS: Specified value was saved.
    4. Quit command prompt by typing exit then pressing [Enter]

This will provide you with both Git and Bash in the Git Bash program.

macOS

The default shell in all versions of macOS 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.

Linux

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.