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# PanGeTools
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```
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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...
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```
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Apptainer container containing useful tools for pangenomics analysis. Versions of tools is reported in the definition file, in the help section.

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# Install
To download the container : 
```
apptainer pull PanGeTools.sif oras://registry.forgemia.inra.fr/alexis.mergez/pangetools/pangetools:latest
```
To execute the container :
```
./PanGeTools.sif <command>
# or
apptainer run --app <cmd name> PanGeTools.sif <cmd args>
```

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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}"
}
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# Alias to update PanGeTools to latest.
alias PGTUp="apptainer build $apptainerpath/PanGeTools.sif oras://registry.forgemia.inra.fr/alexis.mergez/pangetools/pangetools:latest"
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```