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
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
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
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