Rasilab-Spelman Comp Bio internship 2023

• Katharine Chen
• Grace Quarterman
• Christine Bynum
• Rasi Subramaniam's lab at Fred Hutch Cancer Center

Documentation

https://github.com/kychen37/rasilab_spelman_2023/blob/main/notes/gq_and_cb_methodology.md

Project Workflow

• Main workflow details

Useful resources

Markdown

• "What is markdown" and "Why use markdown" sections of this guide
• Markdown is typically used in text editors (like VSCode)
• Note that this document is written in markdown, which automatically renders into the denoted formatting when pushed/opened on github

Command line & terminal

• https://www.technigo.io/explained/what-is-the-terminal
• The terminal (mac/linux) or command prompt (windows) is a way to execute simple commands directly on the files in your computer

Github

• Make an account on github and verify your email address
• Install git to your laptops by following this site
• Clone our group's remote repository to your local computer by opening the terminal and executing the following: git clone https://github.com/kychen37/rasilab_spelman_2023.git
  • Since this repo was made in my account (kychen37), I needed to added gquarter and christinebynum users to the repo on github under Settings before they had permission to push/pull
• Each user needs to then generate a personal access token:
  • Go to your user settings -> Developer settings -> Personal access tokens -> Tokens (classic) -> Generate new token (classic)
  • Under Note, name the token something descriptive and check 'repo'
  • Press Generate token, copy the entire token to a different location like a notepad
• Follow the top comment on https://stackoverflow.com/questions/46645843/where-to-store-my-git-personal-access-token for saving the personal access token to the git credential helper so you don't have to keep copy/pasting it each time you push
  • git config --global user.name "Katharine Chen"
  • git config --global user.email kychen37@uw.edu
  • git config --global credential.helper manager-core
• The default behavior of git is to rebase, but if you don't set it explicitly it will give you an error each time you try to pull, so run:
  • git config --global pull.rebase true
• Now you can run the usual git workflow:
  • git add filename of the file you editted
  • git commit -m "descriptive message about what was editted
  • git push origin main
• You should also do git pull origin main to get any changes to the remote repo that other users may have pushed

R programming

Installing R

• https://rstudio-education.github.io/hopr/starting.html

Programming in python

Installing miniconda:

• What is miniconda?
• Mac: https://docs.conda.io/projects/conda/en/latest/user-guide/install/macos.html
  • Follow the link "Miniconda installer for macOS."
  • Click on the link "Miniconda3 macOS Intel x86 64-bit bash", which will download the installation to your Downloads folder
  • Open terminal and navigate to your Downloads folder (hint cd)
  • Run: sh Miniconda3-latest-MacOSX-x86_64.sh and follow prompts in terminal (say 'yes' to 'conda init' question)
  • After installation is done, close and reopen terminal
  • Run: conda list, which should show a list of packages if the installation was successful (will probably say something like conda not found if it was unsuccessful)
• Windows: https://docs.conda.io/projects/conda/en/latest/user-guide/install/windows.html
  • Open the executable and follow instructions
• After you've finished installing miniconda, install pandas by typing: conda install pandas on the command line
• If you need any more packages down the road, you would run: conda install packagename on the command line
  • e.g. numpy and matplotlib are common python packages, to install them you would run: conda install numpy, conda install matplotlib

VSCode

• A very useful text editing and coding application
• Various extensions make coding/writing in VSCode much easier

Setting up Jupyter kernels in VSCode

• In VSCode, find the Extensions panel
• Search for the extension called Jupyter and download it
• Open a python interactive notebook (called a Jupyter notebook)
  • For Mac: press CMD+SHIFT+P to open the drop-down menu -> click Create Jupyter notebook
• In top right corner: select "Select Kernel" -> "Python environments" -> choose the "base (miniconda3/bin/python)"
• Start coding!
  • The first time you run a code chunk, VSCode may ask you to download some needed additional extensions, download those

Link to Notes/ Checklist

• https://docs.google.com/document/d/1oH2o3IqIo8S2cpuaRkC1sHXC3Qf9WcVbSqiicUIzfk8/edit
• https://docs.google.com/document/d/1pm8s1GsDygkZAIZ5U-h7Nw7eMhKVGkSIK1jx5_jSpuk/edit