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#!/bin/bash
ADDITIONAL_SIMKA_OPTIONS=$*
#simple test with real data
# look for simka binary. In devel mode, it's in ../build/bin directory.
# In production mode, it's in ../bin directory.
bindir="/usr/bin"
# run simka
command="$bindir/simka -in ../example/simka_input.txt -out ./simka_results/ -out-tmp ./simka_temp_output $ADDITIONAL_SIMKA_OPTIONS"
#printf "$command\n\n"
# DO NOT add lines between '$command' exec and 'var...' !
$command
var=$?
printf "\n\n\n"
if [ $var -eq 0 ]
then
echo "*** Test: PASSED"
else
echo "*** Test: FAILED"
exit 1
fi
#printf "\nremoving all created dirs\n"
# clean temp files
rm -rf temp_output
printf "\nCommand used:\n"
printf "\t$command\n"
printf "\nCommand for visualizing results:\n"
printf "\tpython ../scripts/visualization/run-visualization.py -in ./simka_results/ -out ./simka_results/ -pca -heatmap -tree\n"
printf "\nCommand for visualizing results with metadata annotations:\n"
printf "\tpython ../scripts/visualization/run-visualization.py -in ./simka_results/ -out ./simka_results/ -pca -heatmap -tree -metadata-in ../example/dataset_metadata.csv -metadata-variable VARIABLE_1\n"
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