If you call the script from outside the script's directory, the Rscript cannot find the temporary files created by the shell script

[somethingp]

I found a solution to this problem by including the full path of the temporary files to the R script.

I edited around line 118 to get the directory the script is being run from (using pwd) and then appending that to the file names passed on to the R script.

path=`dirname $0`
tempfile_path=`pwd`
if [[ -f $2 ]] && [[ $norm == "norm" ]]
then
	echo "Calculating threshold using normalized control: $(date)"
	Rscript $path/SEACR_1.3.R --exp="$tempfile_path/$password.auc" --ctrl="$tempfile_path/$password2.auc" --norm=yes --output="$tempfile_path/$password"
elif [[ -f $2 ]]
then
	echo "Calculating threshold using non-normalized control: $(date)"
	Rscript $path/SEACR_1.3.R --exp="$tempfile_path/$password.auc" --ctrl="$tempfile_path/$password2.auc" --norm=no --output="$tempfile_path/$password"
else
	echo "Using user-provided threshold: $(date)"
	Rscript $path/SEACR_1.3.R --exp="$tempfile_path/$password.auc" --ctrl=$2 --norm=no --output=$tempfile_path/$password
fi

[mpmeers]

Hello,

Thanks for the heads up here--I will incorporate this into a future version.

Mike