There are several pieces of software you need to install before the workshop. Though installation help will be provided at the workshop, we recommend that these tools are installed (or at least downloaded) beforehand. Anaconda Python is a very large download.
Lesson Data Files
The files used in this lesson can be downloaded:
Once downloaded, please extract to the directory you wish to work in for all the
hands-on exercises. If you are working on the Linux or Mac command-line, you can
do something like the following. We assume you have downloaded the file to
cd mkdir workflow-workshop cd workflow-workshop mv ../Downloads/workflow-engines-lesson.tar.gz . tar xf workflow-engines-lesson.tar.gz
On Windows, please use the Windows Explorer to create a directory and extract the Zip file into it.
Solutions for most episodes can be found in the
.solutions directory inside
the code download.
requirements.txt file is included in the download. As described below,
this can be used to install the required Python packages.
Python 3 / Anaconda
You will need Python 3.6 or better to use the sample files, since some relatively new Python features are used. Instructions are given here for installing Anaconda, although any Python will work.
- Visit the Anaconda download page
- Select your operating system (Windows, macOS, or Linux).
- Download the Python 3 64-bit graphical installer.
- After the download completes, run the installer to install Anaconda.
Follow the Installation Guide
If you need more detailed guidance, then please follow the Anaconda Installation guide.
- Once Anaconda is installed, it is a good idea to update it.
- The article Keeping Anaconda Up To Date is a good guide to updating Anaconda after it is installed.
- It boils down to opening an Anaconda terminal and running the command:
conda update --all
Updating is not essential for this course
If you would rather skip updating, then it is not essential for this course.
The example code also requires the
numpy libraries. They
are installed by default with Anaconda, but if you are using a different
Python you may need to install them manually. Using
pip, the command would
pip install --user numpy matplotlib
The example files download also contains a
requirements.txt file that can
be used to specify the required packages for a Python virtual environment.
There are many guides to this process online, including the official
Once you have Python 3 available, you need to install the Snakemake library.
You can install Snakemake at an Anaconda prompt:
conda install -c bioconda -c conda-forge snakemake-minimal
At the time of writing, the
snakemakeconda package was not installing correctly, however the
snakemake-minimalwas working. This lesson does not require any features beyond those included with the minimal install.
You can install Snakemake with:
pip install --user snakemake
If you used the supplied
requirements.txt to create a Python virtual
snakemake should already be installed. For more information,
please refer to the Snakemake installation
Some of the commands used in this lesson assume that some common Linux commands
are available. These include
tar. These commands are not available
by default on Windows systems. While there are many solutions, including using
the Windows Subsystem for Linux (WSL), a simple approach that we have tested is
to install Git for Windows. This installs a lightweight command-line environment
that contains the required Linux commands and can be configured to use Anaconda
First, download and install the Windows Git client.
Next, make sure you have installed Anaconda as described above.
The final, and critical, step is tell Git Bash where Anaconda is installed, so
that you can use Anaconda Python from Git Bash. First, open an Anaconda terminal
and identify the installation location of Anaconda with this command (if the
which command is not available, please ensure you have installed Git Bash with
all default options):
Take note of the result. It will typically be something like
/c/Users/YourUserName/Anaconda3/Scripts/conda for user installs, and
Now you can add Anaconda to your Git Bash
- Open Git Bash from the Start Menu.
- Using the location of Anaconda you identified in the previous step, run the
- You can replace
- You should not include the trailing
- You can replace
- Run the following command:
Now you are good to go!
Making it Permanent
You will need to repeat the previous three steps everytime you open a new Git Bash shell. If you want to make these changes permanent then you can use the following commands in Git Bash to add the changes to
.bashrcfile (remember to substitute the actual location of your Anaconda installation):
cd echo 'export PATH=$PATH:~/AppData/Local/Continuum/Anaconda3/Scripts' >> .bashrc` echo 'source activate >> .bashrc'
Note that you must use single quotes, not double quotes due to the way that