To go through this tutorial, you need the following software installed:
- Python ≥3.5
- Snakemake ≥5.24.1
- BWA 0.7
- SAMtools 1.9
- Pysam 0.15
- BCFtools 1.9
- Graphviz 2.42
- Jinja2 2.11
- NetworkX 2.5
- Matplotlib 3.3
The easiest way to setup these prerequisites is to use the Miniconda Python 3 distribution. The tutorial assumes that you are using either Linux or MacOS X. Both Snakemake and Miniconda work also under Windows, but the Windows shell is too different to be able to provide generic examples.
Setup on Windows¶
If you already use Linux or MacOS X, go on with Step 1.
Windows Subsystem for Linux¶
If you use Windows 10, you can setup the Windows Subsystem for Linux (WSL) to natively run linux applications. Install the WSL following the instructions in the WSL Documentation. You can chose any Linux distribution available for the WSL, but the most popular and accessible one is Ubuntu. Start the WSL and setup your account; now, you can follow the steps of our tutorial from within your Linux environment in the WSL.
Vagrant virtual machine¶
If you are using a version of Windows older than 10 or if you do not wish to install the WSL, you can instead setup a Linux virtual machine (VM) with Vagrant.
First, install Vagrant following the installation instructions in the Vagrant Documentation.
Then, create a reasonable new directory you want to share with your Linux VM, e.g., create a folder
Open a command line prompt, and change into that directory.
Here, you create a 64-bit Ubuntu Linux environment with
> vagrant init hashicorp/precise64 > vagrant up
If you decide to use a 32-bit image, you will need to download the 32-bit version of Miniconda in the next step.
The contents of the
vagrant-linux folder will be shared with the virtual machine that is set up by vagrant.
You can log into the virtual machine via
> vagrant ssh
If this command tells you to install an SSH client, you can follow the instructions in this Blogpost. Now, you can follow the steps of our tutorial from within your Linux VM.
Step 1: Installing Miniconda 3¶
First, please open a terminal or make sure you are logged into your Vagrant Linux VM. Assuming that you have a 64-bit system, on Linux, download and install Miniconda 3 with
$ wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh $ bash Miniconda3-latest-Linux-x86_64.sh
On MacOS X, download and install with
$ curl https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -o Miniconda3-latest-MacOSX-x86_64.sh $ bash Miniconda3-latest-MacOSX-x86_64.sh
For a 32-bit system, URLs and file names are analogous but without the
When you are asked the question
Do you wish the installer to prepend the Miniconda3 install location to PATH ...? [yes|no]
answer with yes.
Along with a minimal Python 3 environment, Miniconda contains the package manager Conda.
After opening a new terminal, you can use the new
conda command to install software packages and create isolated environments to, e.g., use different versions of the same package.
We will later use Conda to create an isolated environment with all required software for this tutorial.
Step 2: Preparing a working directory¶
First, create a new directory
snakemake-tutorial at a reasonable place and change into that directory in your terminal:
$ mkdir snakemake-tutorial $ cd snakemake-tutorial
If you use a Vagrant Linux VM from Windows as described above, create that directory under
/vagrant/, so that the contents are shared with your host system (you can then edit all files from within Windows with an editor that supports Unix line breaks).
Then, change to the newly created directory.
In this directory, we will later create an example workflow that illustrates the Snakemake syntax and execution environment.
First, we download some example data on which the workflow shall be executed:
$ wget https://github.com/snakemake/snakemake-tutorial-data/archive/v5.24.1.tar.gz $ tar --wildcards -xf v5.24.1.tar.gz --strip 1 "*/data" "*/environment.yaml"
This will create a folder
data and a file
environment.yaml in the working directory.
Step 3: Creating an environment with the required software¶
environment.yaml file can be used to install all required software into an isolated Conda environment with the name
$ conda env create --name snakemake-tutorial --file environment.yaml
Step 4: Activating the environment¶
To activate the
snakemake-tutorial environment, execute
$ conda activate snakemake-tutorial
Now you can use the installed tools. Execute
$ snakemake --help
to test this and get information about the command-line interface of Snakemake. To exit the environment, you can execute
$ conda deactivate
but don’t do that now, since we finally want to start working with Snakemake :-).