Welcome to the 2023 QB Bootcamp of the School for Biological Sciences at Cold Spring Harbor Laboratory! This Github repository contains the Jupyter notebooks, shell scripts, and datasets that we will work through in this bootcamp.
Repository URL: https://github.com/jbkinney/23e_qbbootcamp
Lead Instructor:
- Justin Kinney (jkinney@cshl.edu), Associate Professor
Schedule:
- Day 1: Tuesday, 5 September 2023, 10am - 6pm, Hershey East Room, Hershey Bldg.
- Day 2: Wednesday, 6 September 2023, 1pm - 6pm, Samet Conference Room, Samet Bldg.
- Day 3: Thursday, 7 September 2023, 10am - 6pm, Plimptom Confernece Room, Beckman Bldg.
Students are asked to install the Anaconda distribution of Python 3.9, on their own computers. This is available at https://www.anaconda.com/products/distribution.
Students with Windows laptops must also install the "Git BASH" tool to prepare for the Bootcamp. You can download it by going to https://gitforwindows.org and clicking the Download button. The installation asks many questions but fortunately provides default answers that work well for the course.
We will use GitBash for the "The Unix command line" section and for logging into Elzar, the high-performance computing cluster on campus.
To log into the Elzar cluster, execute this at your command line:
ssh [user]@bamdev2.cshl.edu
where [user] is your CSHL username (e.g. mine is jkinney). Then enter your CSHL password.
To download elzar_exercise.tar.gz to Elzar, execute:
wget --no-check-certificate "https://github.com/jbkinney/23e_qbbootcamp/raw/main/elzar_exercise.tar.gz"
Then to unpack, execute:
tar -zxvf elzar_exercise.tar.gz