PanGeTools
PanGeTools - Pangenomic General tools - Version 1.3.0
This container wraps several tools used for working with pangenomes.
It contains :
- GFAffix v0.1.5
- smoothxg v0.7.2
- odgi v0.8.3
- vg v1.53.0
- panacus v0.2.3
- gfatools v0.5
- GFAvc v0.1
- samtools v1.19
- bgzip v1.19.1
- wfmash v0.10.5
- minimap2 v2.26
Use apptainer --app <toolname> <container_path> [command] to run the selected tool.
Tool names are lowercase : gfaffix, smoothxg, odgi, vg, panacus, etc... Apptainer container containing useful tools for pangenomics analysis. Versions of tools is reported in the definition file, in the help section.
Add the following function to your bashrc to have easier commands :
# Folder containing apptainer images (.sif)
apptainerpath="<path_to_apptainer_folder>"
# Function to easly run PanGeTools.
# The command is PanGeTools <tool name> <tool args>
PanGeTools() {
apptainer run --app $1 $apptainerpath/PanGeTools.sif "${@:2}"
}
# Alias to update PanGeTools to latest.
alias PGTUp="apptainer build $apptainerpath/PanGeTools.sif oras://registry.forgemia.inra.fr/alexis.mergez/pangetools/pangetools:latest"