PanGeTools
PanGeTools - Pangenomic General tools - Version 1.8c
This container wraps several tools used for working with pangenomes.
It contains :
- GFAffix v0.1.5
- smoothxg v0.7.2
- odgi v0.8.6
- vg v1.56.0
- panacus v0.2.3
- gfatools v0.5
- GFAvc v0.3
- GFAstats v0.3.2
- samtools v1.19
- bgzip v1.19.1
- wfmash v0.10.5
- minimap2 v2.26
- vcfbub v0.1.0
- vcflib v1.0.9
- RTG v3.12.1
- Mash v2.3
- pansel v1.0
- GraphAligner v1.0.19
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.
Install
To download the container :
apptainer pull PanGeTools.sif oras://registry.forgemia.inra.fr/alexis.mergez/pangetools/pangetools:latestTo execute the container :
./PanGeTools.sif <command>
# or
apptainer run --app <cmd name> PanGeTools.sif <cmd args>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"