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Building database
Nicolas de Montigny edited this page Jan 12, 2022
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There is a template script to build data in one large fasta file and extract classes into a csv file. This template must be modified by the user to insert filepaths and comment the host section if there is no host to be used.
The modified template can be submited on a HPC cluster managed by Slurm (ex: Compute Canada) using the following command :
sbatch Caribou/data/build_data_scripts/template_slurm_datagen.sh
The modified template can also be ran in a linux command shell by running the following command :
sh Caribou/data/build_data_scripts/template_slurm_datagen.sh
Finally each script used by the template can be used in linux command shell by running the following commands :
sh Caribou/data/build_data_scripts/generateFastaList.sh -d [directory] -o [outputFile]
sh Caribou/data/build_data_scripts/fasta2class_bact.sh -d [directory] -i [inputFile] -c [classesFile] -o [outputDirectory]
sh Caribou/data/build_data_scripts/fasta2class_host.sh -d [directory] -i [inputFile] -o [outputDirectory]