Index: branches/Mars_McMismatchStudy/qsub/FACT.qsub_call_mc.sh
===================================================================
--- branches/Mars_McMismatchStudy/qsub/FACT.qsub_call_mc.sh	(revision 17986)
+++ branches/Mars_McMismatchStudy/qsub/FACT.qsub_call_mc.sh	(revision 17986)
@@ -0,0 +1,14 @@
+#!/bin/bash
+
+
+INFILE=FFFFF
+OUTDIR=DDDDD
+
+TSAMPLES="test300samples2.drs.fits.gz"
+FITSFILE="/gpfs0/fact/monte-carlo/gamma/processing_20140716/CERES/PEDESTAL/00000001.001_P_MonteCarlo000_Events.fits"
+
+source ~/.bash_profile
+
+cd $MARSSYS
+
+root -b -q fact/analysis/mc/callisto.C\(\"$TSAMPLE\", \"FITSFILE\",\"$INFILE\", \"$OUTDIR\"\)
Index: branches/Mars_McMismatchStudy/qsub/FACT.qsub_ceres_mc.sh
===================================================================
--- branches/Mars_McMismatchStudy/qsub/FACT.qsub_ceres_mc.sh	(revision 17985)
+++ branches/Mars_McMismatchStudy/qsub/FACT.qsub_ceres_mc.sh	(revision 17986)
@@ -3,5 +3,6 @@
 
 INFILE=FFFFF
-OUTDOR=DDDDD
+OUTDIR=DDDDD
+LOGFILE=$INFILE".log"
 
 source ~/.bash_profile
@@ -14,2 +15,5 @@
 ./ceres -b -q -f --out=$OUTDIR $INFILE
 
+## PED??
+./ceres -b -q -f --fits --config=ceres.rc --out=$OUTDIR --log=$LOGFILE pedestal
+
Index: branches/Mars_McMismatchStudy/qsub/FACT.qsub_gan_mc.sh
===================================================================
--- branches/Mars_McMismatchStudy/qsub/FACT.qsub_gan_mc.sh	(revision 17986)
+++ branches/Mars_McMismatchStudy/qsub/FACT.qsub_gan_mc.sh	(revision 17986)
@@ -0,0 +1,12 @@
+#!/bin/bash
+
+
+INFILE=FFFFF
+OUTDIR=DDDDD
+
+source ~/.bash_profile
+
+cd $MARSSYS
+
+root -b -q fact/analysis/ganymed.C\(\"$INFILE\",\"$OUTDIR\",5.5755,22.0144,kFALSE\)
+
Index: branches/Mars_McMismatchStudy/qsub/FACT.qsub_ped_mc.sh
===================================================================
--- branches/Mars_McMismatchStudy/qsub/FACT.qsub_ped_mc.sh	(revision 17986)
+++ branches/Mars_McMismatchStudy/qsub/FACT.qsub_ped_mc.sh	(revision 17986)
@@ -0,0 +1,15 @@
+#!/bin/bash
+
+
+INFILE=FFFFF
+OUTDOR=DDDDD
+
+source ~/.bash_profile
+
+cd $MARSSYS
+
+## NO CONFIG FILE??
+##./ceres -b -q -f --config= --out=$OUTDIR $INFILE
+
+./ceres -b -q -f --out=$OUTDIR $INFILE
+
Index: branches/Mars_McMismatchStudy/qsub/FACT.qsub_star_mc.sh
===================================================================
--- branches/Mars_McMismatchStudy/qsub/FACT.qsub_star_mc.sh	(revision 17986)
+++ branches/Mars_McMismatchStudy/qsub/FACT.qsub_star_mc.sh	(revision 17986)
@@ -0,0 +1,14 @@
+#!/bin/bash
+
+
+INFILE=FFFFF
+OUTDIR=DDDDD
+
+source ~/.bash_profile
+
+cd $MARSSYS
+
+## NO CONFIG FILE??
+##./ceres -b -q -f --config= --out=$OUTDIR $INFILE
+
+root -q -b fact/analysis/mc/star.C\(\"$INFILE\", \"$OUTDIR\"\)
Index: branches/Mars_McMismatchStudy/qsub/FACT.sub_call_mc.sh
===================================================================
--- branches/Mars_McMismatchStudy/qsub/FACT.sub_call_mc.sh	(revision 17986)
+++ branches/Mars_McMismatchStudy/qsub/FACT.sub_call_mc.sh	(revision 17986)
@@ -0,0 +1,43 @@
+#!/bin/bash
+
+if [[ $# < 1 ]]
+then
+  echo ""
+  echo "FACT.sub_call_mc.sh <input dir> <output dir>"
+  echo ""
+  exit
+fi
+
+cd $MARSSYS
+
+INDIR=$1
+OUTDIR=$2
+
+TEMPFILE="temp.call.file"
+
+## TODO ths will need fixing
+ls $INDIR/cer* | head -n 1 > $TEMPFILE
+
+while read LINE
+do
+
+  INFILE=$LINE
+
+  NUMBER=`echo $LINE | sed s/cer/" "/g | gawk '{print $2}'`
+
+  QSUB=$MARSSYS"/batch/queue/FACT.qsub_call_mc_"$NUMBER".sh"
+  QSUBERR=$MARSSYS"/batch/queue/FACT.qsub_call_mc_"$NUMBER".err"
+  QSUBOUT=$MARSSYS"/batch/queue/FACT.qsub_call_mc_"$NUMBER".out"
+
+  sed -e "s|FFFFF|$INFILE|"  \
+      -e "s|DDDDD|$OUTDIR|"   $MARSSYS"/batch/FACT.qsub_call_mc.sh" > $QSUB
+
+  chmod +x $QSUB
+
+  qsub -q fact_medium -b yes -o $QSUBOUT -e $QSUBERR $QSUB
+  ##qsub -q test -b yes -o $QSUBOUT -e $QSUBERR $QSUB
+  ##qsub -b yes -o $QSUBOUT -e $QSUBERR $QSUB
+
+done <$TEMPFILE
+
+rm $TEMPFILE
Index: branches/Mars_McMismatchStudy/qsub/FACT.sub_gan_mc.sh
===================================================================
--- branches/Mars_McMismatchStudy/qsub/FACT.sub_gan_mc.sh	(revision 17986)
+++ branches/Mars_McMismatchStudy/qsub/FACT.sub_gan_mc.sh	(revision 17986)
@@ -0,0 +1,46 @@
+#!/bin/bash
+
+if [[ $# < 1 ]]
+then
+  echo ""
+  echo "FACT.sub_gan_mc.sh <input dir> <output dir>"
+  echo ""
+  exit
+fi
+
+cd $MARSSYS
+
+INDIR=$1
+OUTDIR=$2
+
+TEMPFILE="temp.gan.file"
+
+#NEED editing
+# TODO
+ls $INDIR/cer* | head -n 1 > $TEMPFILE
+
+while read LINE
+do
+
+  INFILE=$LINE
+
+#NEED editing
+# TODO
+  NUMBER=`echo $LINE | sed s/cer/" "/g | gawk '{print $2}'`
+
+  QSUB=$MARSSYS"/batch/queue/FACT.qsub_gan_mc_"$NUMBER".sh"
+  QSUBERR=$MARSSYS"/batch/queue/FACT.qsub_gan_mc_"$NUMBER".err"
+  QSUBOUT=$MARSSYS"/batch/queue/FACT.qsub_gan_mc_"$NUMBER".out"
+
+  sed -e "s|FFFFF|$INFILE|"  \
+      -e "s|DDDDD|$OUTDIR|"   $MARSSYS"/batch/FACT.qsub_gan_mc.sh" > $QSUB
+
+  chmod +x $QSUB
+
+  ##qsub -q fact_medium -b yes -o $QSUBOUT -e $QSUBERR $QSUB
+  qsub -q test -b yes -o $QSUBOUT -e $QSUBERR $QSUB
+  ##qsub -b yes -o $QSUBOUT -e $QSUBERR $QSUB
+
+done <$TEMPFILE
+
+rm $TEMPFILE
Index: branches/Mars_McMismatchStudy/qsub/FACT.sub_ped_mc.sh
===================================================================
--- branches/Mars_McMismatchStudy/qsub/FACT.sub_ped_mc.sh	(revision 17986)
+++ branches/Mars_McMismatchStudy/qsub/FACT.sub_ped_mc.sh	(revision 17986)
@@ -0,0 +1,42 @@
+#!/bin/bash
+
+if [[ $# < 1 ]]
+then
+  echo ""
+  echo "FACT.sub_ceres_mc.sh <input dir> <output dir>"
+  echo ""
+  exit
+fi
+
+cd $MARSSYS
+
+INDIR=$1
+OUTDIR=$2
+
+TEMPFILE="temp.ceres.file"
+
+ls $INDIR/cer* | head -n 1 > $TEMPFILE
+
+while read LINE
+do
+
+  INFILE=$LINE
+
+  NUMBER=`echo $LINE | sed s/cer/" "/g | gawk '{print $2}'`
+
+  QSUB=$MARSSYS"/batch/queue/FACT.qsub_ceres_mc_"$NUMBER".sh"
+  QSUBERR=$MARSSYS"/batch/queue/FACT.qsub_ceres_mc_"$NUMBER".err"
+  QSUBOUT=$MARSSYS"/batch/queue/FACT.qsub_ceres_mc_"$NUMBER".out"
+
+  sed -e "s|FFFFF|$INFILE|"  \
+      -e "s|DDDDD|$OUTDIR|"   $MARSSYS"/batch/FACT.qsub_ceres_mc.sh" > $QSUB
+
+  chmod +x $QSUB
+
+  ##qsub -q fact_medium -b yes -o $QSUBOUT -e $QSUBERR $QSUB
+  qsub -q test -b yes -o $QSUBOUT -e $QSUBERR $QSUB
+  ##qsub -b yes -o $QSUBOUT -e $QSUBERR $QSUB
+
+done <$TEMPFILE
+
+rm $TEMPFILE
Index: branches/Mars_McMismatchStudy/qsub/FACT.sub_star_mc.sh
===================================================================
--- branches/Mars_McMismatchStudy/qsub/FACT.sub_star_mc.sh	(revision 17986)
+++ branches/Mars_McMismatchStudy/qsub/FACT.sub_star_mc.sh	(revision 17986)
@@ -0,0 +1,44 @@
+#!/bin/bash
+
+if [[ $# < 1 ]]
+then
+  echo ""
+  echo "FACT.sub_star_mc.sh <input dir> <output dir>"
+  echo ""
+  exit
+fi
+
+cd $MARSSYS
+
+INDIR=$1
+OUTDIR=$2
+
+TEMPFILE="temp.star.file"
+
+## Need to edit this TODO
+ls $INDIR/cer* | head -n 1 > $TEMPFILE
+
+while read LINE
+do
+
+  INFILE=$LINE
+
+## Need to edit this TODO
+  NUMBER=`echo $LINE | sed s/cer/" "/g | gawk '{print $2}'`
+
+  QSUB=$MARSSYS"/batch/queue/FACT.qsub_star_mc_"$NUMBER".sh"
+  QSUBERR=$MARSSYS"/batch/queue/FACT.qsub_star_mc_"$NUMBER".err"
+  QSUBOUT=$MARSSYS"/batch/queue/FACT.qsub_star_mc_"$NUMBER".out"
+
+  sed -e "s|FFFFF|$INFILE|"  \
+      -e "s|DDDDD|$OUTDIR|"   $MARSSYS"/batch/FACT.qsub_star_mc.sh" > $QSUB
+
+  chmod +x $QSUB
+
+  ##qsub -q fact_medium -b yes -o $QSUBOUT -e $QSUBERR $QSUB
+  qsub -q test -b yes -o $QSUBOUT -e $QSUBERR $QSUB
+  ##qsub -b yes -o $QSUBOUT -e $QSUBERR $QSUB
+
+done <$TEMPFILE
+
+rm $TEMPFILE