Today we’re going to spend most of our time getting setup with all of the tools we’ll be using throughout the semester. While we’re going through these various activities, please check off the different tasks after you’ve completed them and at the end, you’ll push your changes to your github repo.

Objectives

  • Get familiar with the SCC OnDemand and VSCode interfaces
  • Setup your SSH key on the SCC with GitHub
  • Edit your ~/.condarc file to change where your conda packages are stored
  • Install the required VSCode plugins
  • Confirm your email and Github ID in the provided form

SCC and SCC OnDemand

Lecture (10 minutes) Computational Skills Primer

Activity (5 minutes)

Ensure you can do the following in VSCode:

  • Open a terminal
  • Create new files and directories
  • Open a new directory as the working directory

git / github

Lecture (10 minutes) git / GitHub

Activity (10 minutes)

We will walk through it together live but if you’re more comfortable following written instructions, please setup a SSH key by following the directions here

This SSH key will pair your SCC account and github repo and allow you to perform basic git operations (push and pull) from the command line without having to enter a password every time.

  • Successfully setup a SSH key
  • Accept and clone the github classroom link

Conda

Lecture (10 minutes) Computational environments and conda

Activity (10 minutes)

We will walk through this together live but if you more comfortable following written instructions, please edit your .condarc according to the directions here

  • Changed where conda stores packages from your home directory to your space on /projectnb/bf528/

After you have completed the above tasks, please run the following command to create your first conda environment:

conda env create -f envs/nextflow_env.yml

As you can see, you must run this command from the root directory of your repo and it will build a conda environment from the provided to you.

This will make a conda environment named “nextflow_env” which you will be using throughout the semester.

Objectives for today

  • Confirm your email and Github ID in the provided form
  • Familiarize yourself with SCC OnDemand and VSCode
  • Setup your SSH key on the SCC with GitHub
  • Edit your ~/.condarc file to change where your conda packages are stored

Install the following VsCode plugins:

  • R extension for Visual Studio Code (REditorSupport)
  • Jupyter (ms-toolsai)
  • Nextflow (nextflow)
  • Python (ms-python)
  • Snakemake Language (snakemake)

Check off the boxes and push your changes to your remote repo.

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