/
procd.sh
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/
procd.sh
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#!/bin/bash
#
# procd copies the outputs of a batch processing run to the project's ${procdir}/${project} directory
# when available, the pipeline txt file containing the stdout from the associated processing pipeline is also copied for sbatch runs
#
# SHOULD also copy the project xml file produced by project_doc.sh as applicable, along with pipeline xml files describing the steps of the pipelines
#
# when the pipeline has been previously run on the dataset, procd will create a new version of the folder with the date appended to distinguish between runs
#
# usage: procd.sh {project} {step} {batch? (yes/no=default)} {subject}
#
# example procd.sh MBB fmriprep yes sub-MBB001
#copying xcpengine fails due to session
project=$1
step=$2
batch=$3
subject=$4
based=$5
session=$6
now=$(date +"%m-%d-%Y-%T")
#switch to version
forkdir=${based}/beta/testing
procdir=${based}/beta/output
if [ -d "$procdir" ];
then
echo "Sending data to $procdir"
else
mkdir $procdir
chmod 777 -R $procdir
fi
if [ "${batch}" == yes ];
then
if [ -d ${procdir}/${project} ];
then
if [ -d ${procdir}/${project}/bids ];
then
if [ -d ${procdir}/${project}/bids/derivatives/${step} ];
then
cp -R ${forkdir}/${project}/bids/derivatives/${step} ${procdir}/${project}/bids/derivatives/${step}_${now}
else
cp -R ${forkdir}/${project}/bids/derivatives/${step} ${procdir}/${project}/bids/derivatives/
fi
else
cp -R ${forkdir}/${project}/bids ${procdir}/${project}/
fi
else
mkdir ${procdir}/${project}
cp -R ${forkdir}/${project}/bids ${procdir}/${project}/
fi
echo ${now} > ${procdir}/${project}/${project}_${step}_doc.txt
else
if [ -d ${procdir}/${project} ];
then
if [ -d ${procdir}/${project}/bids ];
then
cp -R ${forkdir}/${project}/bids/derivatives/${step}/${subject} ${procdir}/${project}/bids/derivatives/${step}/${subject}
else
cp -R ${forkdir}/${project}/bids ${procdir}/${project}/
fi
else
mkdir ${procdir}/${project}
cp -R ${forkdir}/${project}/bids ${procdir}/${project}/
fi
echo ${now} > ${procdir}/${project}/${project}_${step}_doc.txt
fi