Small updates of scripts based on ShellCheck advice.

Author: V-Z

presentation/linux_bash_metacentrum_course.tex

@@ -3600,7 +3600,7 @@ \subsection{Reading variables}
       echo "  for multiplication or quotient for quotient."
       exit 1 # End up with an error
       }
-    if [ "$#" -ne "3" ]; then # Do we have 3 parameters provided?
+    if [[ "$#" -ne "3" ]]; then # Do we have 3 parameters provided?
       echo "Error! Requiring 3 parameters! Received $# ($*)."
       usagehelp # The function to print help
       fi # "=~" means testing if $1 fits to regular expression in $NUMBER
@@ -3683,8 +3683,8 @@ \subsection{Reading variables}
           ;; # End of this option
         a) # Parameter "-a" accepts some value (e.g. "-a X" for number)
           # Check if provided value makes sense (integer between 10 and 300)
-          if [[ "$OPTARG" =~ ^[0-9]+$ ]] && [ "$OPTARG" -ge 10 ] &&
-            [ "$OPTARG" -le 300 ]; then # The condition is long...
+          if [[ "$OPTARG" =~ ^[0-9]+$ ]] && [[ "$OPTARG" -ge 10 ]] &&
+            [[ "$OPTARG" -le 300 ]]; then # The condition is long...
             VALUE=$OPTARG # $OPTARG always contains value of parameter
             echo "Value is OK: $VALUE"
             else
@@ -3708,7 +3708,7 @@ \subsection{Reading variables}
         esac
       done # ...the end.
     # Check if all required values are provided
-    if [ -z "$INPUTFILE" ] || [ -z "$OUTPUTFILE" ]; then
+    if [[ -z "$INPUTFILE" ]] || [[ -z "$OUTPUTFILE" ]]; then
       echo "Error! Name of input and/or output file was not provided!"
       echo "See \"$0 -h\" for help usage..."
       exit 1
@@ -3720,7 +3720,7 @@ \subsection{Reading variables}
 \begin{frame}[fragile]{Multiple switches in classical UNIX form (no positional) IV}
 	\begin{bashcode}
     # ...continuing from previous slide...
-    if [ -z "$VALUE" ]; then
+    if [[ -z "$VALUE" ]]; then
       echo "Warning! Value for \"-a\" was not provided! Using default (10)."
       VALUE=10
       fi
@@ -3764,12 +3764,12 @@ \subsection{Reading variables}
 	\begin{bashcode}
     #!/bin/bash
     # We expect exactly one parameter
-    if [ "$#" -ne "1" ]; then
+    if [[ "$#" -ne "1" ]]; then
       echo "Error! Exactly one parameter is required!"
       exit 1
       fi
     # Verify that file exists and is readable
-    if [ ! -r "$1" ]; then
+    if [[ ! -r "$1" ]]; then
       echo "Error! The file provided does not exist or is not readable!"
       exit 1
       fi

scripts_data/interactive4.sh

@@ -12,7 +12,7 @@ function usagehelp {
 	}
 
 # Do we have 3 parameters provided?
-if [ "$#" -ne "3" ]; then
+if [[ "$#" -ne "3" ]]; then
 	echo "Error! Requiring 3 parameters! Received $# ($*)."
 	usagehelp # The function to print help
 	fi

scripts_data/interactive5.sh

@@ -13,7 +13,7 @@ while getopts "hvi:o:a:" INITARGS; do
 			exit # Terminate after providing help
 			;; # End of this option
 		i) # Parameter "-i" accepts some value (e.g. "-i inputfile.txt")
-			if [ -r "${OPTARG}" ]; then # Check if the input file exists and is readable
+			if [[ -r "${OPTARG}" ]]; then # Check if the input file exists and is readable
 				echo "OK, File \"${OPTARG}\" exists and is readable. Proceeding..."
 				INPUTFILE="${OPTARG}" # $OPTARG always contains value of parameter
 				else
@@ -23,7 +23,7 @@ while getopts "hvi:o:a:" INITARGS; do
 				fi
 			;; # End of this option
 		o) # Parameter "-o" accepts some value (e.g. "-o outputfile.txt")
-			if [ -n "${OPTARG}" ]; then # Check if there is some name for output variable
+			if [[ -n "${OPTARG}" ]]; then # Check if there is some name for output variable
 				echo "OK, Name for output file was provided: \"${OPTARG}\". Proceeding..."
 				OUTPUTFILE="${OPTARG}" # $OPTARG always contains value of parameter
 				else
@@ -34,7 +34,7 @@ while getopts "hvi:o:a:" INITARGS; do
 			;; # End of this option
 		a) # Parameter "-a" accepts some value (e.g. "-a X" for number)
 			# Check if provided value makes sense (integer between 10 and 300)
-			if [[ "${OPTARG}" =~ ^[0-9]+$ ]] && [ "${OPTARG}" -ge 10 ] && [ "${OPTARG}" -le 300 ]; then # The condition is long...
+			if [[ "${OPTARG}" =~ ^[0-9]+$ ]] && [[ "${OPTARG}" -ge 10 ]] && [[ "${OPTARG}" -le 300 ]]; then # The condition is long...
 				VALUE=${OPTARG} # $OPTARG always contains value of parameter
 				echo "Value is OK: ${VALUE}"
 				else
@@ -52,14 +52,14 @@ done
 
 # Check if all required values are provided
 
-if [ -z "${INPUTFILE}" ] || [ -z "${OUTPUTFILE}" ]; then
+if [[ -z "${INPUTFILE}" ]] || [[ -z "${OUTPUTFILE}" ]]; then
 	echo "Error! Name of input and/or output file was not provided!"
 	echo "See \"$0 -h\" for help usage..."
 	echo
 	exit 1
 	fi
 
-if [ -z "${VALUE}" ]; then
+if [[ -z "${VALUE}" ]]; then
 	echo "Warning! Value for \"-a\" was not provided! Using default value of 10."
 	VALUE=10
 	fi

scripts_data/interactive6.sh

@@ -1,13 +1,13 @@
 #!/bin/bash
 
 # We expect exactly one parameter
-if [ "$#" -ne "1" ]; then
+if [[ "$#" -ne "1" ]]; then
 	echo "Error! Exactly one parameter is required!"
 	exit 1
 	fi
 
 # Verify that file exists and is readable
-if [ ! -r "$1" ]; then
+if [[ ! -r "$1" ]]; then
 	echo "Error! The file provided does not exist or is not readable!"
 	exit 1
 	fi

scripts_data/metacentrum_oxalis.sh

@@ -16,7 +16,7 @@ trap 'cp -a "${SCRATCHDIR}" "${DATADIR}"/ && clean_scratch' TERM
 
 # Required modules
 echo "Loading module(s)"
-module add iqtree-1.6.12 || exit 1 # iqtree
+module add iqtree-1.6.12 || exit 1
 echo
 
 # Change working directory
@@ -31,7 +31,7 @@ cp -a "${DATADIR}"/"${DATAFSA}" "${SCRATCHDIR}"/ || exit 1
 echo
 
 echo "Computing gene tree from ${DATAFSA}..."
-iqtree -s "${DATAFSA}" -st DNA -nt 1 -m MFP+I+R+P -lmap ALL -cmax 1000 -nstop 1000 -alrt 10000 -bb 10000 -bnni || exit 1
+iqtree -s "${DATAFSA}" -st DNA -nt 1 -m MFP+I+R+P -lmap ALL -cmax 1000 -nstop 1000 -alrt 10000 -bb 10000 -bnni || { export CLEAN_SCRATCH='false'; exit 1; }
 echo
 
 # Copy results back to home directory