Merge branch 'fixesForManual' of git@gitlab.com:rootmodels/OpenSimRoot.git into fixesForManual

#!/bin/bash

# this script creates in an ../Output/ folder for every runXXXX.xml file in the InputFiles Folder

# a seperate folder and submits that file to the cluster to be run

# if you want to exlcude files, rename or remove them from the InputFolder

# if you want to run different maize configurations, add for each a runMaizeXXX.xml folder in the InputFiles. 

pushd ../../../../ > /dev/null

make nopython

pushd > /dev/null

rsync ../../../../nopython_build/OpenSimRoot_noPython OpenSimRoot

list=` find ../../../InputFiles/ -name "run*.xml" -execdir  basename -as .xml {} \;`

cnt=0;

for i in $list ; do

   folder="../Output/$i/"

   echo "Setting up $folder"

#   mkdir -p $folder

#   rsync -a ../../../InputFiles $folder

#   rsync job.sh $folder

   pushd $folder > /dev/null

#   rsync "InputFiles/$i.xml" InputFiles/runModel.xml

   qsub -N "$i" job.sh

   pushd  > /dev/null

done