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|
#!/bin/bash
set -e
pkg=aevol
if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
# Double quote below to expand the temporary directory variable now versus
# later is on purpose.
# shellcheck disable=SC2064
trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
fi
cp /usr/share/doc/${pkg}/examples/* -a "${AUTOPKGTEST_TMP}"
cd "${AUTOPKGTEST_TMP}"
gunzip -r *
# Run simulation
cd workflow/wild_type
aevol_create
xvfb-run --auto-servernum --server-args="-screen 0 1024x768x24" aevol_run -n 100 -p -1
# 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 $outdirsC
do
xvfb-run --auto-servernum --server-args="-screen 0 1024x768x24" aevol_propagate -o ../$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
xvfb-run --auto-servernum --server-args="-screen 0 1024x768x24" aevol_modify -f ../newparam-groupA.in
cd ..
done
for mydir in $outdirsB
do
cd $mydir
xvfb-run --auto-servernum --server-args="-screen 0 1024x768x24" aevol_modify -f ../newparam-groupB.in
cd ..
done
for mydir in $outdirsC
do
cd $mydir
xvfb-run --auto-servernum --server-args="-screen 0 1024x768x24" aevol_modify -f ../newparam-groupC.in
cd ..
done
# Run the simulations
#
for mydir in $outdirsA $outdirsB $outdirsC
do
cd $mydir
xvfb-run --auto-servernum --server-args="-screen 0 1024x768x24" 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
# FIXME: Added '|| true' since this test contains errors
# We want to see those errors in the test logs but
# it should not make the whole test fail
aevol_misc_lineage || true
cd ..
done
# aevol_misc_ancstats
for mydir in $outdirsA $outdirsB $outdirsC
do
cd $mydir
aevol_misc_ancestor_stats lineage-*.ae -M &
cd ..
done
|
