Installation

Linux

pip install -e git+https://github.com/dmnfarrell/snipgenie.git#egg=snipgenie

Notes: You may need to use pip3 on Ubuntu to ensure you use Python 3. Running this also requires you have git installed. The same command can be used to update to the latest version.

WSL on Windows

The tool can be run on Windows using Windows Subsystem for Linux (WSL). This is easy to install from the Micrsoft store. (You can also run `wsl --install' from a terminal window). You then install Ubuntu 22.04 LTS from the store. Just make sure your version of Windows 10 is also reasonably up to date.

Open Ubuntu from the start menu and run it. It will bring up a terminal. This is just like being in normal Linux. You should first install some required packages:

sudo apt install python3-pip x11-apps libqt5extras5

You can then install the app using pip as above.

Dependencies

For Linux installs, you require Python 3 and the following packages. These will be installed automatically when using pip.

• numpy
• pandas
• matplotlib
• biopython
• pyvcf3
• pyfaidx
• pyqt5 (GUI only)
• toytree (GUI only)

Other binaries required:

• bwa
• samtools
• bcftools
• tabix
• parallel

These binaries can be installed with apt in Ubuntu:

sudo apt install bwa samtools bcftools tabix parallel

If you want a tree to be built you should install RaXML, but it's optional:

sudo apt install raxml

Test it's working

To test things are working you can run snipgenie -T. This will generate some artificial fastq files and run the workflow on them. The results will be saved in the current folder under 'test_run_results'.