From e0802340137e9eb2df1d1561a7be5cf421fd03e9 Mon Sep 17 00:00:00 2001
From: Fengchao <fcyucn@gmail.com>
Date: Mon, 22 Jul 2024 20:12:40 -0400
Subject: [PATCH] Add a tutorial about pulling and running FragPipe using
 Docker

https://github.com/Nesvilab/FragPipe/issues/1690
---
 README.md               |  1 +
 docs/tutorial_docker.md | 10 ++++++++++
 2 files changed, 11 insertions(+)
 create mode 100644 docs/tutorial_docker.md

diff --git a/README.md b/README.md
index 771beffd4..7eae3db94 100644
--- a/README.md
+++ b/README.md
@@ -13,6 +13,7 @@ FragPipe is a comprehensive computational platform for analyzing mass spectromet
 #### FragPipe tutorials
 * [Using FragPipe](https://fragpipe.nesvilab.org/docs/tutorial_fragpipe.html) (general tutorial covering all FragPipe modules)
 * [Running FragPipe in command line interface](https://fragpipe.nesvilab.org/docs/tutorial_headless.html)
+* [Pulling and running FragPipe using Docker](https://fragpipe.nesvilab.org/docs/tutorial_docker.html)
 * PTM discovery
   * [Open search](https://fragpipe.nesvilab.org/docs/tutorial_open.html)
   * [Mass offset search](https://fragpipe.nesvilab.org/docs/tutorial_offset.html)
diff --git a/docs/tutorial_docker.md b/docs/tutorial_docker.md
new file mode 100644
index 000000000..3f6ace578
--- /dev/null
+++ b/docs/tutorial_docker.md
@@ -0,0 +1,10 @@
+# Pulling and running FragPipe using Docker
+
+- Install docker by following the [instruction](https://docs.docker.com/desktop/install/mac-install/)
+- Open terminal and pull the docker image: `docker pull fcyucn/fragpipe`
+- (optional) Check the pulled image: `docker image ls -a`
+- Create a Docker container: `docker run -it -v <host directory>:<container directory> fcyucn/fragpipe /bin/bash`. `<host directory>` is the directory in your host machine, and `<container directory>` is the directory you want to map the host directory to container.
+- Then, you have entered the docker, and FragPipe is located in `/fragpipe_bin`
+- Go to `/fragpipe_bin/fragPipe-x.x/fragpipe/bin` directory and execute `./fragpipe --help` in the terminal
+
+Read more: Check [Running FragPipe in command line interface](https://fragpipe.nesvilab.org/docs/tutorial_headless.html) for the instructions running FragPipe in command line interface.