I am trying to transfer a pipeline from one server to another one. I am having some issues with some of the bash scripts in the new server and I was wondering if there is any package that I need to install to get around them.
For example I have a script that looks like this:
#!/bin/bash -l
#$ -cwd
# file name: pipeline.sh
code="path_to_code"
# fastq files
f1=$2 # R1
f2=$3 # R2
# libType = N or S
findType1=`echo $f1 | grep "ONE\|TWO\|THREE" | wc -c`
findType2=`echo $f1 | grep "FOUR\|FIVE\|SIX" | wc -c`
if [[ $findType1 -gt 0 ]]; then
libType="S"
elif [[ $findType2 -gt 0 ]]; then
libType="N"
else
echo "unable to determine the library type of $f1 - exitting!"
exit 12
fi
echo $libType
echo $f1
echo $f2
# SE (single end)
if [[ $f2 == "" ]]; then
sh $code/Mapping.sh -l "$libType" -f "$f1" -p "NA"
else
sh $code/Mapping.sh -l "$libType" -f "$f1" -p "$f2"
fi
On the old server this script works fine. However, to get it to work on the new server I had to replace any "[[" with "[". In addition, I had to replace "==" with "=". Can anyone tell me why I am having these issues?
I have tried running the script both as sh path/to/script.sh and as bash path/to/script.sh but I am getting the same error.
Thank you