Installing Ensembl VEP via Podman Desktop

This guide walks you through installing Ensembl Variant Effect Predictor (VEP) using Podman Desktop on Windows, Mac or Linux. Podman is an open-source tool that can be used to run containers for software. Podman can pull images from hubs of containers such as Docker Hub.

Containers are lightweight, portable software packages that bundle a tool and all its dependencies into a self-contained environment, making analyses with tools like Ensembl VEP easy to install, run reproducibly on any system, and share with others.

System requirements

Prerequisites

Check the minimum system requirements for Podman Desktop:

Installing Podman Desktop

Download Podman Desktop for your system

Follow the Podman Desktop installation guide for your system

Installing Ensembl VEP on Podman Desktop

Ensembl VEP can be installed via the Podman Desktop software, or directly via the command-line. Use one of the following instructions to install Ensembl VEP via Podman:

Via the Podman Desktop software:
1. Open Podman Desktop
2. Go to Images
3. Select Pull
4. Enter ensemblorg/ensembl-vep
5. Select Pull Image
6. Click Run
7. Select Start Container
Via your Terminal (for Mac and Linux only):
1. Open a Terminal window
2. Run the following command
```
podman pull ensemblorg/ensembl-vep
```

Reference: Ensembl VEP on DockerHub

Running Ensembl VEP

Windows

Getting started

Open Windows PowerShell. You can do so by searching PowerShell in the Windows Start Menu.
Inside PowerShell, create a working directory for Ensembl VEP data by running the following command:

mkdir $HOME\vep_data

Download example files and add them to the working directory

Download example files from the Ensembl VEP GitHub repository either via an internet browser or via Git:

Downloading via an internet browser:
1. Open an internet browser
2. Go to the Ensembl VEP GitHub repository
3. In the top right-hand corner, click the green <> Code button
4. Select Download ZIP, save it into the vep_data working directory you just created
5. Uncompress the ZIP file inside vep_data
Downloading via Git:
1. Open Windows PowerShell
2. Navigate to your working directory by running the following command:
```
cd $HOME\vep_data
```
1. Download the Ensembl VEP repo by running the following command:
```
git clone https://github.com/Ensembl/ensembl-vep.git
```

Run Podman with mounted directory

In PowerShell, run Podman with the mounted directory using the following command:

podman run -t -i -v $HOME\vep_data:/data ensemblorg/ensembl-vep

Inside the container, you can fetch the required files using curl once Ensembl VEP is started. Test the tool by running the following command:

vep –help

You will the following message:

#----------------------------------#
# ENSEMBL VARIANT EFFECT PREDICTOR #
#----------------------------------#

You can close the interactive run with the key combination [crtl]+[D].

Mac and Linux

Getting started

Open a Terminal window
Create a working directory for your Ensembl VEP data:

mkdir ~\vep_data

Download example files and add them to the working directory

Download example files from the Ensembl VEP GitHub repository either via an internet browser or via Git:

Downloading via an internet browser:
1. Open an internet browser
2. Go to the Ensembl VEP GitHub repository
3. In the top right-hand corner, click the green <> Code button
4. Select Download ZIP and save it into the vep_data working directory you just created
5. Uncompress the ZIP file inside vep_data

Downloading via Git:
1. Open a Terminal window
2. Navigate to your working directory by running the following command:
```
cd ~\vep_data
```
1. Download the Ensembl VEP repo by running the following command:
```
git clone https://github.com/Ensembl/ensembl-vep.git
```

Run Podman with mounted directory

In a Terminal window, run Podman with the mounted directory using the following command:

podman run -t -i -v $HOME/vep_data:/data ensemblorg/ensembl-vep

Inside the container, you can fetch the required files using curl once Ensembl VEP is started. Test the tool by running the following command:

vep –help

You will the following message:

#----------------------------------#
# ENSEMBL VARIANT EFFECT PREDICTOR #
#----------------------------------#

You can close the interactive run with the key combination [crtl]+[D].

Helpful resources

Ensembl VEP References

Ensembl VEP container on DockerHub
- Installation and requirements
Running Ensembl VEP
- Basic Ensembl VEP commands
- Example Ensembl VEP scripts
- Ensembl VEP plugins (advanced use)

Notes for UNIX commands

Ensembl VEP commands assume a UNIX-based environment.

Common UNIX commands include:

Command	Action
ls	List all files in current directory
cd [directoryName]	Change to directory [directoryName]
mkdir [directoryName]	Create directory [directoryName]
curl URL -o [fileName]	Download file [fileName]

Here are some useful references for learning basic UNIX commands: