Installation

We provide binaries for the latest version of PanGenie under Releases. Alternatively, PanGenie can be installed with conda:

conda install bioconda::pangenie

However, if you prefer to build PanGenie yourself, follow the instructions below.

Building from source using Singularity (recommended)

Use the Singularity definition file located here to build an (Ubuntu-based) container as follows (requires root privileges):

[sudo] singularity build pangenie.sif pangenie.def

In all usage examples below, call the PanGenie executables as follows:

singularity exec pangenie.sif PanGenie-index <PARAMETERS>
singularity exec pangenie.sif PanGenie <PARAMETERS>

For example, to show PanGenie’s command line help, use the following command:

singularity exec pangenie.sif PanGenie --help

You can check which versions of PanGenie (git hash) and of the jellyfish library have been installed in the container by running the following commands:

singularity exec pangenie.sif cat /metadata/jellyfish.lib.version

should produce a line like this (so, here, v2.3.0):

$ libjellyfish-2.0-2:amd64 2.3.0-4build1 libjellyfish-2.0-dev:amd64 2.3.0-4build1

singularity exec pangenie.sif cat /metadata/pangenie.git.version

should produce a line like this:

$ 5a1f9c5

Building from source using Conda

git clone https://github.com/eblerjana/pangenie.git
cd pangenie
conda env create -f environment.yml
conda activate pangenie
mkdir build; cd build; cmake .. ; make

Building from source

This requires Jellyfish and cereal to be installed.

git clone https://github.com/eblerjana/pangenie.git
cd pangenie
mkdir build; cd build; cmake .. ; make