BAM/runBAM.sh at main · HassounLab/BAM · GitHub

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#!/bin/bash

molecules_of_interest="./data/input/GMN_validation_dataset.csv"
SOM_DIRECTORY='./GNN-SOM-master/'
WRITE_DIRECTORY='./data/output/'

######KEGG biotransformations
metabolites_list="./data/reactions/KEGG/KEGG_metabolite_input.csv"
reaction_list="./data/reactions/KEGG/KEGG_reactions.csv"
OP_CACHE_DIRECTORY='./data/reactions/KEGG/operators'
path_finalReactions='./data/reactions/KEGG/'

######RetroRules biotransformations
#metabolites_list="./data/reactions/RetroRules/RetroRules_metabolite_input.csv"
#reaction_list="./data/reactions/RetroRules/RetroRules_reactions.csv"
#OP_CACHE_DIRECTORY='./data/reactions/RetroRules/operators'
#path_finalReactions='./data/reactions/RetroRules/'

conda run -n proximal2 python ./main/runPROX2.py --moi "$molecules_of_interest" --som_dir "$SOM_DIRECTORY" --write_dir "$WRITE_DIRECTORY" --rxn_mets "$metabolites_list" --rxns "$reaction_list" --op_dir "$OP_CACHE_DIRECTORY" --rxn_dir "$path_finalReactions" >> out_BAM_PROX2.txt

conda run -n gnn_som python ./main/runSOM.py --moi "$molecules_of_interest" --som_dir "$SOM_DIRECTORY" --write_dir "$WRITE_DIRECTORY" --rxn_dir "$path_finalReactions" >> out_BAM_SOM.txt