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Snakemake Usage

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1- Activate conda an environment containing snakemake. To create environment following instruction here :

## Use conda

https://snakemake.readthedocs.io/en/stable/getting_started/installation.html

1- Get a list of fish to analyze

+ This should be a sublist of the Tulane metadata -> https://bgnn.tulane.edu/hdrweb/hdr/imagemetadata/

+ There is demo list in the main folder : List/list_lepomis_INHS.csv

2- cd in the main folder

cd BGNN_Snakemake

3- Execute snakemake file

The following instruction will automatically call snakefile using snakemake, use <1> cores and use the <list_lepomis_INHS.csv>

snakemake --cores 1 --use-singularity --config list=List/list_lepomis_INHS.csv

SBATCH_ACCOUNT = PAS2136

sinteractive -N 1 -n 4 -t 00:10:00 -A PAS2136 -J test -p debug squeue -u thibaulttabarin

snakemake --cores 4 --use-singularity --config list=List/list_lepomis_INHS.csv

snakemake --cores 4 --use-singularity --config list=list_test.csv