error while running a R script in a bash script - r

Question

e made a bash script as follows:
#! /bin/bash
OUTDIR=".//DATA/share/pipelines/results/"
INDIR="./DATA/share/pipelines/test_data/infile/"
projectname=$1
input_bam=$2
bins=$3
mkdir OUTDIR || true
of="${OUTDIR}"
ind="${INDIR}"
./DATA/share/pipelines/script.R \
-b "${bins}" \
-c "${projectname}" \
-o "${of}" \
-i "${ind}"
echo "first step is done"
when I run the script using the following command:
bash first.sh 30 beh
I will get this error:
mkdir: cannot create directory ‘OUTDIR’: File exists
first.sh: line 17: ./DATA/share/pipelines/script.R: No such file or directory
first step is done
do you know how to solve the problem?

Answer 1

When you call
bash first.sh 30 beh
$1 holds 30, $2 holds beh and $3 is not defined.
input_bam ist set to $2 but is never used.
With [ ! -d ${OUTDIR} ] you should be able to test if the directory exists.
#! /bin/bash
#Please check if it should be
# relative to the current working directory (starting with './')
# or absolute (starting with '/')
BASEDIR="/DATA/share/pipelines/" #"./DATA/share/pipelines/"
OUTDIR=${BASEDIR}"results/"
INDIR=${BASEDIR}"test_data/infile/"
projectname=$1
input_bam=$2 #This is never used
bins=$3 #This is not defined when callin >bash first.sh 30 beh<
[ ! -d ${OUTDIR} ] && mkdir ${OUTDIR} #Think you would create ${OUTDIR}
of="${OUTDIR}"
ind="${INDIR}"
./DATA/share/pipelines/script.R \
-b "${bins}" \
-c "${projectname}" \
-o "${of}" \
-i "${ind}"
echo "first step is done"