v0.8.7

MANUAL.md

@@ -3,6 +3,7 @@
 ## About
 
 This manual is meant to clarify the most important options and possibilities when running *vcf2gwas*.  
+**Note**: When running *vcf2gwas* via [docker](https://www.docker.com/), replace `vcf2gwas` in every command with `docker run -v /path/to/current-working-directory/:/vcf2gwas/ fvogt257/vcf2gwas`.  
 To obtain example files for running *vcf2gwas*, run:
 
 ```

README.md

@@ -9,7 +9,8 @@
     * [Built With](#built-with)
 * [Getting Started](#getting-started)
     * [Prerequisites](#prerequisites)
-    * [Installation](#installation)
+    * [Installation via conda](#installation-via-conda)
+    * [Installation via docker](#installation-via-docker)
 * [Usage](#usage)
     * [Input Files](#input-files)
     * [Running *vcf2gwas*](#running-vcf2gwas)
@@ -56,13 +57,13 @@ The exact versions of [Python](https://www.python.org/), [bcftools](http://samto
 ## Getting Started
 
 These instructions will provide an easy way to get *vcf2gwas* running on your local machine.  
-*vcf2gwas* works on macOS and Linux systems.
+*vcf2gwas* works on macOS and Linux systems when run via [conda](https://conda.io/projects/conda/en/latest/user-guide/install/index.html). When running the [*vcf2gwas* docker image](https://hub.docker.com/r/fvogt257/vcf2gwas), *vcf2gwas* runs on all operating systems supported by [docker](https://www.docker.com/).
 
 ### Prerequisites
 
-The only requirement is an up to date version of [conda](https://conda.io/projects/conda/en/latest/user-guide/install/index.html) installed on your machine.
+The only requirement is an up to date version of either [conda](https://conda.io/projects/conda/en/latest/user-guide/install/index.html) or [docker](https://www.docker.com/products/docker-desktop/) installed on your machine.
 
-### Installation
+### Installation via conda
 
 It is a good practice to install the package in a clean environment.  
 So first create a new environment (you can name it as you like), here with the exemplary name 'myenv':
@@ -96,6 +97,21 @@ Once the analysis is completed, the environment can be deactivated:
 conda deactivate
 ```
 
+### Installation via docker
+
+To download the [*vcf2gwas* docker image](https://hub.docker.com/r/fvogt257/vcf2gwas),  run the following command:
+
+```
+docker pull fvogt257/vcf2gwas
+```
+
+Everything is ready for analysis now.  
+Optionally, to test the image and copy the example files to your current working directory, run:
+
+```
+docker run -v /path/to/current-working-directory/:/vcf2gwas/ fvogt257/vcf2gwas -v test
+```
+
 ## Usage
 
 The items below will explain the required format of the input files, the basic usage and available options as well as the structure of the output files.
@@ -150,6 +166,12 @@ Once the virtual environment is activated, *vcf2gwas* can be run on the command-
 vcf2gwas -v example.vcf.gz -pf example.csv -ap -lmm
 ```
 
+**Note**: When running *vcf2gwas* via [docker](https://www.docker.com/), replace in every command `vcf2gwas` with `docker run -v /path/to/current-working-directory/:/vcf2gwas/ fvogt257/vcf2gwas`:
+
+```
+docker run -v /path/to/current-working-directory/:/vcf2gwas/ fvogt257/vcf2gwas -v example.vcf.gz -pf example.csv -ap -lmm
+```
+
 The available options will be elucidated in the next section.  
 In the [manual](https://github.com/frankvogt/vcf2gwas/blob/main/MANUAL.md), detailed instructions on how to run *vcf2gwas* and its available options can be viewed.