OpenScience master script v1.0

OpenScience.sh

+#!/bin/bash -e
+#################### WIN OpenScience Wrapper version 6.0.1 ##############
+#########################################################################
+### This script expects to be run in a directory where the user has
+### read-write access, all files generated by this script will be
+### created in that directory.
+#################### Standard set-up functions ##########################
+DEFAULTDIR=`pwd`
+#### Usage
+function usage {
+    echo "$0: [-d] [-f] [-o]"
+    echo "OpenScience wrapped version of an analysis."
+    echo "-d <directory>: Use existing data in <directory> instead of downloading"
+    echo "-f <directory>: Use existing FSL in <directory> instead of downloading"
+    echo "-o <directory>: Output to <directory> instead of current directory"
+    echo ""
+}
+##### FSL - Download
+function downloadFSL {
+    echo "Installing FSL via internet"
+    curl -s https://fsl.fmrib.ox.ac.uk/fsldownloads/fslinstaller.py > fslinstaller.py
+    chmod u+x fslinstaller.py
+    ./fslinstaller.py -V 6.0.1 -q -p -d $1
+}
+##### FSL - Setup
+function setupFSL {
+    echo "Setting up FSL"
+    if [ $# -eq 0 ]; then
+        NEWFSLDIR=${DEFAULTDIR}/fsl
+        downloadFSL ${NEWFSLDIR}
+    else
+        NEWFSLDIR=$1
+    fi
+    if [ ! -z "${FSLDIR}" ]; then
+        PATH=${PATH/$FSLDIR/}
+    fi
+    export FSLDIR=${NEWFSLDIR}
+    export PATH=${FSLDIR}/bin:${PATH}
+    . ${FSLDIR}/etc/fslconf/fsl.sh
+}
+##### Data - Setup
+function setupData {
+    echo "Setting up data"
+    if [ $# -gt 1 ]; then
+        DATADIR=$2
+        return
+    fi
+    echo "Downloading data via internet"
+    curl -s $1 | tar -zxf -
+    DATADIR=${DEFAULTDIR}
+}
+#################### Standard OpenScience entrypoint ####################
+OUTPUTDIR=${DEFAULTDIR}
+unset existingFSLDIR
+unset existingDATADIR
+while getopts "f:d:o:" Option
+do
+    case $Option in
+    d   )
+        existingDATADIR=$OPTARG
+	    ;;
+    f   )
+	    existingFSLDIR=$OPTARG
+	    ;;
+    o   )
+        OUTPUTDIR=$OPTARG
+        ;;
+    *   )
+        usage
+        exit 1
+	    ;;
+    esac
+done
+#################### Analysis-specific URL ############################
+DATAURL='https://users.fmrib.ox.ac.uk/~mwebster/data2.tar.gz'
+#################### Setup Environment ################################
+setupFSL ${existingFSLDIR}
+setupData ${DATAURL} ${existingDATADIR}
+#################### Start of data processing #########################
+echo "Starting analysis"
+echo "with FSLDIR:${FSLDIR} DATADIR:${DATADIR} OUTPUTDIR:${OUTPUTDIR}"
+#################### Analysis-specific commands #######################
+${FSLDIR}/bin/bet ${DATADIR}/structural ${OUTPUTDIR}/structural_brain -f 0.5 -g 0 -m -s
+${DATADIR}/scripts/myScript.sh ${OUTPUTDIR}/structural_brain > myOutput.txt
+#################### End of Analysis ##################################
+echo "Done"
+#################### End of data processing ###########################