adding a LOG-fn to log output, also setting the WORKINGdir using absolute paths to account for relative references to it from the command line args

diff --git a/core/countReads.sh b/core/countReads.sh
index bfaf860..159a222 100755
--- a/core/countReads.sh
+++ b/core/countReads.sh
@@ -34,27 +34,37 @@ startTime=`date +%s`
 ###############################


-### STARTING LOG ##############
+### LOG function ##############
 logging() {
-        # set log file
+        # set log file
         LOG_FILE=${myDIR}/"racs_${RunTimeDir}.log"
-        # open log file
-        touch ${LOG_FILE}
-        # capture std.output
-        #exec 1> ${LOG_FILE}
-	# capture std.error
-	#exec 2>&1
+        # open log file
+        touch ${LOG_FILE}
+
+	# CAPTURING standard output/error and still displaying in 'screen' (std.output)
+        # capture std.output
+        #exec 1> ${LOG_FILE}
+	exec 1> >(tee -a ${LOG_FILE} >&1)
+	# capture std.error
+	exec 2>&1
 	# capture std. error and also mirror it to screen
-        exec 1> ${LOG_FILE} 2> >(tee -a ${LOG_FILE} >&2)
+        #exec 1> ${LOG_FILE} 2> >(tee -a ${LOG_FILE} >&1)
+	exec 2> >(tee -a ${LOG_FILE} >&1)
 	# other ways...
-        # >&3 | tee /dev/tty
-        #{ { echo out; echo err 1>&2; } 2>&1 >&3 | tee /dev/tty; } >log 3>&1
-        # exec 1>log 2> >(tee -a log >&2)
-
-        ###
-        welcome
-        echo $0 $@
-        date
+        # >&3 | tee /dev/tty
+        ###{ { echo out; echo err 1>&2; } 2>&1 >&3 | tee /dev/tty; } >${LOG_FILE} 3>&1
+        #exec 1> ${LOG_FILE} 2> >(tee -a ${LOG_FILE} >&2)
+
+	###
+	# display welcome line about RACS
+        welcome
+	echo ""
+	# include original issued command passed as an argument to this fn
+        echo " cmd>>> " $@
+	echo ""
+	# print date
+        date
+	echo ".................."
 }
 ################################

@@ -130,7 +140,7 @@ inputFILE2=IPfile
 #RAMdisk=/dev/shm/$USER/
 #RAMdisk=/tmp/$USER/
 RunTimeDir=ORF_RACS-$$-`date '+%Y%m%d-%H%M%S'`
-[ -d $5 ] && WORKINGdir=$5/$USER/$RunTimeDir || errMsg "6th argument must be a directory, we suggest using /dev/shm for RAMdisk or /tmp in a SSD device, as this pipeline is quite I/O intense!"
+[ -d $5 ] && WORKINGdir=$( cd "$5" && pwd )/$USER/$RunTimeDir || errMsg "6th argument must be a directory, we suggest using /dev/shm for RAMdisk or /tmp in a SSD device, as this pipeline is quite I/O intense!"
 echo "Working directory --> " $WORKINGdir


@@ -195,7 +205,8 @@ tableIPs=tableReadsIP.`basename $IPfile .fastq.gz`

 ####=====================================================

-logging
+# begin outputing to LOG file...
+logging $0$@

 ## pipeline
 # index the assembly
@@ -295,6 +306,8 @@ endTime=`date +%s`

 runtime=$((endTime-startTime))

+echo "-----------------------------"
 echo "Total runtime: $runtime secs"
+echo "-----------------------------"

 ################################