Tried to automatize difference checks with check-diffs.sh.

default.conf

@@ -29,12 +29,12 @@ length_cutoff	0.8						minimum sequence length expressed in number of residues
 >Software
 clustalW	/usr/local/bin/clustalw2			clustalW system dependent command
 muscle          /usr/bin/muscle                                 muscle system dependent command
-naccess		/home/tekpinar/research/carbone-lab-software/naccess2.1.1/naccess 	naccess system dependent command
+naccess		/home/tekpinar/research/lcqb/naccess2.1.1/naccess 	naccess system dependent command
 psiblast	/usr/bin/psiblast				psiblast system dependent command
 
 *****************************************
 >Data
-substMatrix	/home/tekpinar/research/carbone-lab-software/JET2/matrix	directory location of matrices used in JET (Blosum62, gonnet and hsdm)
+substMatrix	/home/tekpinar/research/lcqb/JET2/matrix	directory location of matrices used in JET (Blosum62, gonnet and hsdm)
 blastDatabases	/opt/blastdb					directory location of databases used for local blast (nr{0-7})
 
 *****************************************
@@ -58,9 +58,9 @@ max_dist        20.0                                            max distance
 >Interface
 cutoff		0         					minimum percentage accessible surface variation of an interface residu
 ligand		no						(yes|no) keep contact of ligand (SUBSTRATE, PRODUCT and COFACTOR of database ENZYME) to compute interface of protein
-enzymeCpd	/home/tekpinar/research/carbone-lab-software/JET2/jet/data/enzyme.txt			location of file containing database ENZYME
+enzymeCpd	/home/tekpinar/research/lcqb/JET2/jet/data/enzyme.txt			location of file containing database ENZYME
 homologousPDB	no						(yes|no) add interface residues of homologous structures (find in pdb database clustered at 95% of identities) to interface of protein
-clusteredPDB	/home/tekpinar/research/carbone-lab-software/JET2/jet/data/clusters95.txt		location of pdb database clustered at 95% of identities
+clusteredPDB	/home/tekpinar/research/lcqb/JET2/jet/data/clusters95.txt		location of pdb database clustered at 95% of identities
 
 *****************************************
 >Cluster

example/check-diffs.sh

+#!/bin/bash
+#Tested with diff (GNU diffutils) 3.7 on an Ubuntu 20.04
+
+
+fileList=(BLAT_pred_evolInd.txt
+	  BLAT_pred_evolEpi.txt
+	  BLAT_normPred_evolInd.txt
+	  BLAT_normPred_evolEpi.txt
+	  BLAT_normPred_evolCombi.txt)
+
+echo "Performing reproducibility checks!"
+#Include the entire trajectory
+for file in ${fileList[@]}
+do
+
+    echo " "
+    diff $file ../tests/$file > /dev/null 2>&1
+    error=$?
+    if [ $error -eq 0 ]
+    then
+	echo "$file and ../tests/$file are same!"
+    elif [ $error -eq 1 ]
+    then
+	echo "$file and ../tests/$file differ!"
+    else
+	echo "There was something wrong with the diff command!"
+    fi
+done

example/example-gemme-script.sh

@@ -3,14 +3,26 @@
 if [ "$1" == "clean" ]
 then
     echo "Cleaning the folder."
+    # rm -rf BLAT_*.txt
+    # rm -rf BLAT_*.png
+    # rm -rf BLAT.pdb
+    # rm -rf BLAT.fasta
     rm -rf BLAT*
     rm -f default.conf caracTest.dat
+
+elif [ "$1" == "jetoff" ]
+then
+    # If you have your own JET2 score file, you can turn off JET2 as follows:
+    # In ../tests folder, you can find a sample JET2 file called BLAT_jet.res 
+    echo "Running GEMME with a user-provided alignment file."
+    echo "Using a previously produced prot_jet.res file to check reproducibility!"
+    cp ../tests/BLAT_jet.res .
+    python $GEMME_PATH/gemme.py aliBLAT.fasta -r input -f aliBLAT.fasta --isjet2on false
+    
 else
     echo "Running GEMME with a user-provided alignment file."
     python $GEMME_PATH/gemme.py aliBLAT.fasta -r input -f aliBLAT.fasta
+    
 fi
 
 
-# If you have your own JET2 score file, you can turn off JET2 as follows:
-# python $GEMME_PATH/gemme.py aliBLAT.fasta -r input -f aliBLAT.fasta --isjet2on false
-# This option can be useful for testing reproducibility!