Update run_tests.sh

Kalan-Lab · Jul 4, 2024 · b4e307d · b4e307d
1 parent c4de247
commit b4e307d
Showing 1 changed file with 4 additions and 1 deletion.
diff --git a/run_tests.sh b/run_tests.sh
@@ -9,7 +9,7 @@ cd test_case/
 prepTG -i Target_Genomes/ -o prepTG_Database/ -c 4 -cst
 
 # Step 2a: run fai (input type 1) to identify orthologous instances of epa from E. faecalis
-fai -i Epa_MIBiG_GBK/Epa_MIBiG_GenBank.gbk -tg prepTG_Database/ -o fai_Results_1/ -c 4 --generate_plots
+fai -i Epa_MIBiG_GBK/Epa_MIBiG_GenBank.gbk -tg prepTG_Database/ -o fai_Results_1/ -c 4 --generate_plots -gdm HMM
 
 # Step 2b: run fai (input type 2) to identify orthologous instances of epa from E. faecalis
 fai -r Efaecalis_V583_Genome.fasta -rc NC_004668.1 -rs 2083902 -re 2115174 -tg prepTG_Database/ -o fai_Results_2/ -c 4 --generate_plots
@@ -19,3 +19,6 @@ fai -pq Epa_Proteins_from_MIBiG_GenBank.faa -tg prepTG_Database/ -o fai_Results_
 
 # Step 3: run zol to perform comparative investigations of gene-clusters
 zol -i fai_Results_2/Final_Results/Homologous_Gene_Cluster_GenBanks/ -o zol_Results/ -c 4 --full_genbank_labels
+
+# Step 4: test out cgc for visualization generation
+cgc -i zol_Results/ -o cgc_Results/