============== 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 singularity exec pangenie.sif PanGenie 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