From e43221e50c35c21bb9419d1e51bb75130146d25b Mon Sep 17 00:00:00 2001
From: KristinaGomoryova <423436@mail.muni.cz>
Date: Mon, 15 Apr 2024 15:31:05 +0200
Subject: [PATCH] README updated

---
 README.md | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/README.md b/README.md
index f8ebe90..91e37f0 100644
--- a/README.md
+++ b/README.md
@@ -12,6 +12,30 @@ The application was written in R, version 4.3.1, using [Shiny library](https://s
 
 The application can be run also locally, using the model dataset, which is a part of already published manuscript.
 
+# Quick start (for Bryjalab)
+
+**Important** Docker image needs to be built locally, it won't work with the virtual instance!! If any changes in 
+`app.R`, `data-preparation.R` or `updateGeneNames.R` scripts are done, docker image needs to be built again.
+
+Docker image can be built (locally using PowerShell) with:
+`docker build -t kristinagomoryova/app:1.0.1 .` (adjust the versioning!)
+
+`docker push kristinagomoryova/app:1.0.1`
+
+Then on the VM:
+
+`docker pull kristinagomoryova/app:1.0.1`
+
+If you change any of the scripts, don't forget to do also `git pull` to update the repository.
+
+**To add new dataset:**
+
+1. Copy the dataset in the VM `\database` folder (e.g. using `mc` commander)
+2. Adjust the metadata.csv file in the `\database` folder (add new record, it's not needed to run metadata.R)
+3. Run the `updateGeneNames.R` script using `Rscript updateGeneNames.R`. Gene names in all files will be automatically updated.
+4. Run the `data-preparation.R` script using `Rscript data-preparation.R` 
+5. Run the `docker run -p 3838:3838 -v /home/ubuntu/MS_shiny_bryjalab/database/:/app/database/ kristinagomoryova/app:1.0.1`. Pay attention to backslashes and versioning of the docker image.
+
 # How to run the application
 
 **Running the model data**: