Use the working script to debug

# Just for debugging

set -x

# Test 1

# Run simulation

cd wild_type

aevol_create

aevol_run -n 50 -p -1

aevol_run -n 100 -p -1

# Test 2

# Test setup

outdirsA="line01 line02 line03 line04 line05"

outdirsB="line06 line07 line08 line09 line10"

outdirsC="line11 line12 line13 line14 line15"

for mydir in $outdirsA $outdirsB $outdirsC

do

  aevol_propagate -o ../$mydir

done

cd ..

# For each experiment, create a file with the parameters to change

echo "# New environment

ENV_GAUSSIAN  0.5   0.2   0.05

ENV_GAUSSIAN  0.5   0.4   0.05

ENV_GAUSSIAN  0.5   0.8   0.05

ENV_VARIATION none

# New rearrangement rates

DUPLICATION_RATE    1e-4

DELETION_RATE       1e-4

TRANSLOCATION_RATE  1e-4

INVERSION_RATE      1e-4" > newparam-groupA.in

echo "# New environment

ENV_GAUSSIAN  0.5   0.2   0.05

ENV_GAUSSIAN  0.5   0.4   0.05

ENV_GAUSSIAN  0.5   0.8   0.05

ENV_VARIATION none

# New rearrangement rates

DUPLICATION_RATE    1e-6

DELETION_RATE       1e-6

TRANSLOCATION_RATE  1e-6

INVERSION_RATE      1e-6" > newparam-groupB.in

echo "# New environment

ENV_GAUSSIAN  0.5   0.2   0.05

ENV_GAUSSIAN  0.5   0.4   0.05

ENV_GAUSSIAN  0.5   0.8   0.05

ENV_VARIATION none" > newparam-groupC.in

# Apply these modifications

#

for mydir in $outdirsA

do

   cd $mydir

   aevol_modify -f ../newparam-groupA.in

   cd ..

done

for mydir in $outdirsB

do

  cd $mydir

  aevol_modify -f ../newparam-groupB.in

  cd ..

done

for mydir in $outdirsC

do

  cd $mydir

  aevol_modify -f ../newparam-groupC.in

  cd ..

done

# Run the simulations

#

for mydir in $outdirsA $outdirsB $outdirsC

do

  cd $mydir

  aevol_run -e 200 -p -1

  cd ..

done

# aevol_misc_create_eps 

for mydir in $outdirsA $outdirsB $outdirsC

do

  cd $mydir

  aevol_misc_create_eps &

  cd ..

done

# aevol_misc_robustness 

for mydir in $outdirsA $outdirsB $outdirsC

do

   cd $mydir

   aevol_misc_robustness &

   cd ..

done

# aevol_misc_lineage 

for mydir in $outdirsA $outdirsB $outdirsC

do

   cd $mydir

   aevol_misc_lineage

   cd ..

done

# aevol_misc_ancstats 

for mydir in $outdirsA $outdirsB $outdirsC

do

   cd $mydir

   aevol_misc_ancestor_stats lineage-*.ae -M &

   cd ..

done

# Test 3