From 30e4410413ad4383da6846bbbd537eaf743e67b7 Mon Sep 17 00:00:00 2001
From: Kdreval <k.dreval@gmail.com>
Date: Thu, 1 Feb 2024 11:00:42 -0800
Subject: [PATCH] new feature: add readme

---
 README.md | 35 +++++++++++++++++++++++++++++++++++
 1 file changed, 35 insertions(+)

diff --git a/README.md b/README.md
index 6fffe32..ebef2b1 100644
--- a/README.md
+++ b/README.md
@@ -1,2 +1,37 @@
 # GAMBLR.viz
+
 Collection of functions to make plots for Genomic Analysis of Mature B-cell Lymphomas in R
+
+# Contributing
+
+## Cloning repo for the code development
+
+The easiest way to obtain and contribute to GAMBLR.viz is to do this via cloning the repository
+
+```
+cd
+git clone git@github.com:morinlab/GAMBLR.viz.git
+```
+
+In your R editor of choice, set your working directory to the place you just cloned the repo.
+
+```
+setwd("~/GAMBLR.viz")
+```
+
+Install the package in R by running the following command (requires the devtools package)
+
+```
+devtools::install()
+```
+
+As GAMBL users (GAMBLRs, so to speak) rely on the functionality of this package, the Master branch is protected. All commits must be submitted via pull request on a branch. Please refer to the [GAMBL](https://github.com/morinlab/gambl#contribution-guidelines) documentation for details on how to do this.
+
+## Function conflicts
+
+This package relies on the use of some functions (e.g. `get_gambl_metadata()`, `get_coding_ssm()` etc) that exist in 2 different versions: [GAMBLR.data](https://github.com/morinlab/GAMBLR.data) for the users who do not have access to GSC and [GAMBLR.results](https://github.com/morinlab/GAMBLR.results) for the Morin Lab users with access to GSC. If your contribution relies on the use of such functions, please follow these 2 steps:
+
+* *DO NOT* prepend the function use with `<package>::` (for example, `<package>::function()`), and
+* *DO NOT* add the corresponding package to the `@import` section of the function
+
+Following these steps will ensure correct usage of the proper function depending on which package is loaded in the session and will avoid functionality conflicts.