added wrapper script

wrapper/wrapper.sh

@@ -0,0 +1,51 @@
+#!/bin/bash
+
+function debug {
+  echo "creating debugging directory"
+mkdir .debug
+for word in ${rmthis}
+  do
+    if [[ "${word}" == *.sh ]] || [[ "${word}" == lib ]]
+      then
+        mv "${word}" .debug;
+      fi
+  done
+}
+
+rmthis=`ls`
+echo ${rmthis}
+
+ARGSU="${columns}"
+INPUTSU="${tab_file}"
+echo "arguments are "${ARGSU}
+echo "inputs are "${INPUTSU}
+
+COLU=\$"${columns}"
+COLU=`echo ${COLU} | sed -e 's/,/,\\$/g'`
+CMDLINEARG="awk '{ print "$COLU" }' IFS='\\t' OFS='\\t' "${INPUTSU}" >> filtered_"${INPUTSU}" "
+
+echo ${CMDLINEARG};
+chmod +x launch.sh
+
+echo  universe                = docker >> lib/condorSubmitEdit.htc
+echo docker_image            =  ubuntu:16.04 >> lib/condorSubmitEdit.htc ######
+echo executable               =  ./launch.sh >> lib/condorSubmitEdit.htc #####
+echo arguments                          = ${CMDLINEARG} >> lib/condorSubmitEdit.htc
+echo transfer_input_files = ${INPUTSU}, launch.sh >> lib/condorSubmitEdit.htc
+#echo transfer_output_files = output >> lib/condorSubmitEdit.htc
+cat /mnt/data/apps/cut_columns/lib/condorSubmit.htc >> lib/condorSubmitEdit.htc
+
+less lib/condorSubmitEdit.htc
+
+jobid=`condor_submit -batch-name ${PWD##*/} lib/condorSubmitEdit.htc`
+jobid=`echo $jobid | sed -e 's/Sub.*uster //'`
+jobid=`echo $jobid | sed -e 's/\.//'`
+
+#echo $jobid
+
+#echo going to monitor job $jobid
+condor_tail -f $jobid
+
+debug
+
+exit 0