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Genouis.sh
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Genouis.sh
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#!/bin/bash
#geneious --options-for De_Novo_Assemble --filter "Log"
#Report option results.saveReport True
#Reads option results.saveUnusedReads true
#geneious -i "LOCAL:Dowload/AMAD/" --operation De_Novo_Assemble -o "C:/Users/clere/OneDrive/Bureau/Genius/AMADOutput.geneious"
#geneious -i "LOCAL:Dowload/AMAD/" --operation De_Novo_Assemble --options "results.saveReport=true" "results.saveUnusedReads=true" -o "C:/Users/clere/OneDrive/Bureau/Genius/AMADOutput.geneious"
# Path to the CSV file containing folder names
CSV_FILE="C:\Users\clere\OneDrive\Bureau\Dowload\ListLakeName.txt"
# Read each line in the CSV file
while IFS=, read -r folder_name; do
# Skip the header line if present
if [ "$folder_name" == "Nom" ]; then
continue
fi
# Construct the input and output paths
input_path="LOCAL:Dowload/${folder_name}/"
#output_path="C:/Users/clere/OneDrive/Bureau/Genius/${folder_name}Output.geneious"
output_path="LOCAL:Dowload/OutPut/${folder_name}Out.geneious"
# Execute the Geneious command
geneious -i "$input_path" --operation De_Novo_Assemble --options "results.saveReport=true" "results.saveUnusedReads=true" -o "$output_path"
#geneious -i "$input_path" --operation De_Novo_Assemble --options "results.saveReport=true" "results.saveUnusedReads=true" "results.generateConsensusSequencesDeNovo=true" "results.consensus.consensusSource=generateFromContig" -o "$output_path"
done < "$CSV_FILE"