Software Dependencies and Pre-requisites

Author

Jenny Smith

Overview

This page contains README’s and internal lab documentation on how to contribute to the Meshinchi lab and Locatelli lab github organizations. Be sure to have the software requirements installed in order to use this guide.

Operating System

These steps can be followed using a Linux operating system, like Ubuntu, or on macbook with MacOS.

Important

Team members with Windows PCs will need to use WSL to follow these installation instructions.

Software

We will be using R, Python, git, gh, and Quarto, with the integrated development editors (IDE) Rstudio and VSCode. Click on the links below to install the required software.

Alternatively, use Posit cloud (formerly Rstudio Cloud). Posit cloud is free of charge for personal users, yet you need to sign up for a new user account and have internet connection.

Git and Github

To get started, you will need to authenticate your access to the lab github organization so that you can create repositories and push changes.

Important

Your github account (also known as your github profile), must be invited to the lab github organization before this can be completed.

  1. Set-up a Github Account and get added as a member to the Lab organization

Github profiles should have a clear/professional profile photo to ensure that profiles look complete and reliable. Also, each account will need to set-up 2FA (2 factor authentication).

  1. Configure git for your github username and email account associated with your github account.

Open a new a new terminal and enter the following commands.

# print out the current configuration 
git config --global --list
# if not already set, configure them. This example assumes you are using a gmail account.
git config --global user.name MY_GITHUB_USERNAME
git config --global user.email MY_GITHUB_EMAIL@gmail.com
git config --global init.defaultbranch main
  1. Authenticate the gh CLI tool to connect to the lab github organization.

Enter the following commands in the terminal. You will be prompted to ? Authenticate Git with your GitHub credentials? (Y/n) and select ‘Yes’. Follow the prompts on the command line to open a new web browser window to enter your username and password for github.

# login to github using a web browser
gh auth login --git-protocol 'HTTPS' --hostname GitHub.com --web

# check that you are now authenticated
gh auth status

Once you see this message that you are logged in, you were successfully authenticated.

✓ Logged in to github.com account MY_GITHUB_USERNAME (keyring) - Active account: true - Git operations protocol: https - Token: gho_************************************ - Token scopes: ‘gist’, ‘read:org’, ‘repo’, ‘workflow’

Data

The lab NGS datasets we use can be found here (insert link).

Code

The R and Python packages, scripts, analysis notebooks, and data processing pipelines can be found at the Meshichi Lab github organization.

Repositories have the following nomenclature for easy searching:

  • Data Analysis and Research Projects with collaborators:

    • [YEAR.MONTH.DAY]_[DATA-TYPE]_[SHORT-DESCRIPTION]

      • Example: ‘2025.06.02_RNAseq_Bulk_T-ALL’

      • Example with two data types: ‘2025.06.02_RNAseq_WGS_Bulk_T-ALL’

  • Genomic Data pipelines and workflows:

    • [DATA-TYPE]_[DATA-PROCESSING]_[WORKFLOW-TYPE]

      • Example: ‘RNAseq_Fusion_Calling_Nextflow’

  • R packages:

    • [SHORT-NAME]_R_Package

      • Example: ‘DeGSEA_R_Package’

  • Python packages:

    • [SHORT-NAME]_Py_Package

      • Example: ‘DataValidator_Py_Package’

Getting Started

See the Getting Started page for the next steps to generate a new analysis or workflow code repository on the github.

If you still need to gain a working knowledge of using bash, R, and Python, then see the following Resources section below.

Resources

Bash and Command Line Tutorial

A good place to start getting familair with common bash commands is to read the following tutorial. Be sure to complete the exercises in the box at the bottom of each page, starting with the ls command.

For more intermediate bash scripting, you can follow the tutorial here.s

Quarto and Visual Studio Code Quick Start

The quarto CLI with VS Code editor quick start is a great tutorial to get familiarized with using quarto (.qmd) documents to generate exploratory analysis notebooks and reports.

R and Rstudio Tutorial

The RStudio user guide can help you get started with the RStudio user interface, installing your first packages, and generating a quick plot using data.

Detailed descriptions of the RStudio panels, panes, and tabsets can be found here as well.

Python Tutorial

Start by learning how the VS Code editor displays and runs python code.

Next, you can follow along with the python tutorial using both the VS Code editor and interactively in a web browser by using the ‘try it yourself’ buttons.