I have a couple of R scripts that processes data in a particular input folder. I have a few folders I need to run this script on, so I started writing a bash script to loop through these folders and run those R scripts.

I'm not familiar with R at all (the script was written by a previous worker and it's basically a black box for me), and I'm inexperienced with passing variables through scripts, especially involving multiple languages. There's also an issue present when I call source("$SWS_output/Step_1_Setup.R") here - R isn't reading my $SWS_output as a variable, but rather a string.

Here's my bash script:

#!/bin/bash

# Inputs
workspace="`pwd`"
preprocessed="$workspace/6_preprocessed"

# Output
SWS_output="$workspace/7_SKSattempt4_results/"

# create output directory
mkdir -p $SWS_output

# Copy data from preprocessed to SWS_output
cp -a $preprocessed/* $SWS_output

# Loop through folders in the output and run the R code on each folder
for qdir in $SWS_output/*/; do
        qdir_name=`basename $qdir`
        echo -e 'source("$SWS_output/Step_1_Setup.R") \n source("$SWS_output/(Step_2_data.R") \n  q()' | R --no-save

done

I need to pass the variable "qdir" into the second R script (Step_2_data.R) to tell it which folder to process.

Thanks!

I have a couple of R scripts that processes data in a particular input folder. I have a few folders I need to run this script on, so I started writing a bash script to loop through these folders and run those R scripts.

I'm not familiar with R at all (the script was written by a previous worker and it's basically a black box for me), and I'm inexperienced with passing variables through scripts, especially involving multiple languages. There's also an issue present when I call source("$SWS_output/Step_1_Setup.R") here - R isn't reading my $SWS_output as a variable, but rather a string.

Here's my bash script:

#!/bin/bash

# Inputs
workspace="`pwd`"
preprocessed="$workspace/6_preprocessed"

# Output
SWS_output="$workspace/7_SKSattempt4_results/"

# create output directory
mkdir -p $SWS_output

# Copy data from preprocessed to SWS_output
cp -a $preprocessed/* $SWS_output

# Loop through folders in the output and run the R code on each folder
for qdir in $SWS_output/*/; do
        qdir_name=`basename $qdir`
        echo -e 'source("$SWS_output/Step_1_Setup.R") \n source("$SWS_output/(Step_2_data.R") \n  q()' | R --no-save

done

I need to pass the variable "qdir" into the second R script (Step_2_data.R) to tell it which folder to process.

Thanks!

I have a couple of R scripts that processes data in a particular input folder. I have a few folders I need to run this script on, so I started writing a bash script to loop through these folders and run those R scripts.

I'm not familiar with R at all (the script was written by a previous worker and it's basically a black box for me), and I'm inexperienced with passing variables through scripts, especially involving multiple languages. Here's my bash script:

#!/bin/bash

# Inputs
workspace="`pwd`"
preprocessed="$workspace/6_preprocessed"

# Output
SWS_output="$workspace/7_SKSattempt4_results/"

# create output directory
mkdir -p $SWS_output

# Copy data from preprocessed to SWS_output
cp -a $preprocessed/* $SWS_output

# Loop through folders in the output and run the R code on each folder
for qdir in $SWS_output/*/; do
        qdir_name=`basename $qdir`
        echo -e 'source("$SWS_output/Step_1_Setup.R") \n source("$SWS_output/(Step_2_data.R") \n  q()' | R --no-save

done

I need to pass the variable "qdir" into the second R script (Step_2_data.R) to tell it which folder to process.

Thanks!

I have a couple of R scripts that processes data in a particular input folder. I have a few folders I need to run this script on, so I started writing a bash script to loop through these folders and run those R scripts.

I'm not familiar with R at all (the script was written by a previous worker and it's basically a black box for me), and I'm inexperienced with passing variables through scripts, especially involving multiple languages. There's also an issue present when I call source("$SWS_output/Step_1_Setup.R") here - R isn't reading my $SWS_output as a variable, but rather a string.

Here's my bash script:

#!/bin/bash

# Inputs
workspace="`pwd`"
preprocessed="$workspace/6_preprocessed"

# Output
SWS_output="$workspace/7_SKSattempt4_results/"

# create output directory
mkdir -p $SWS_output

# Copy data from preprocessed to SWS_output
cp -a $preprocessed/* $SWS_output

# Loop through folders in the output and run the R code on each folder
for qdir in $SWS_output/*/; do
        qdir_name=`basename $qdir`
        echo -e 'source("$SWS_output/Step_1_Setup.R") \n source("$SWS_output/(Step_2_data.R") \n  q()' | R --no-save

done

I need to pass the variable "qdir" into the second R script (Step_2_data.R) to tell it which folder to process.

Thanks!

I have a couple of R scripts that processes data in a particular input folder. I have a few folders I need to run this script on, so I started writing a bash script to loop through these folders and run those R scripts.

I'm not familiar with R at all (the script was written by a previous worker and it's basically a black box for me), and I'm inexperienced with passing variables through scripts, especially involving multiple languages. Here's my bash script:

#!/bin/bash

Inputs

workspace="pwd" preprocessed="$workspace/6_preprocessed"

Output

SWS_output="$workspace/7_SKSattempt4_results/"

create output directory

mkdir -p $SWS_output

Copy data from preprocessed to SWS_output

cp -a $preprocessed/* $SWS_output

Loop through folders in the output and run the R code on each folder

for qdir in $SWS_output/*/; do qdir_name=basename $qdir echo -e 'source("$SWS_output/Step_1_Setup.R") \n source("$SWS_output/(Step_2_data.R") \n q()' | R --no-save

done

I need to pass the variable "qdir" into the second R script (Step_2_data.R) to tell it which folder to process.

Thanks!

I have a couple of R scripts that processes data in a particular input folder. I have a few folders I need to run this script on, so I started writing a bash script to loop through these folders and run those R scripts.

I'm not familiar with R at all (the script was written by a previous worker and it's basically a black box for me), and I'm inexperienced with passing variables through scripts, especially involving multiple languages. Here's my bash script:

#!/bin/bash

# Inputs
workspace="`pwd`"
preprocessed="$workspace/6_preprocessed"

# Output
SWS_output="$workspace/7_SKSattempt4_results/"

# create output directory
mkdir -p $SWS_output

# Copy data from preprocessed to SWS_output
cp -a $preprocessed/* $SWS_output

# Loop through folders in the output and run the R code on each folder
for qdir in $SWS_output/*/; do
        qdir_name=`basename $qdir`
        echo -e 'source("$SWS_output/Step_1_Setup.R") \n source("$SWS_output/(Step_2_data.R") \n  q()' | R --no-save

done

I need to pass the variable "qdir" into the second R script (Step_2_data.R) to tell it which folder to process.

Thanks!