shellcheck.sh

du.sh

@@ -1,5 +1,5 @@
 #!/bin/bash --noprofile
-THIS=`dirname $0`
+THIS=$( dirname $0 )
 source $THIS/bash_common.sh
 if [ $# -ne 1 ]; then
   echo "Print total file size in M bytes"

grid_wait.sh

@@ -1,5 +1,5 @@
 #!/bin/bash --noprofile
-THIS=`dirname $0`
+THIS=$( dirname $0 )
 source $THIS/bash_common.sh
 if [ $# -ne 1 ]; then
   echo "Wait until UGE is available"
@@ -23,7 +23,7 @@ while true; do
     break
   fi
   sleep 60
-  N=$(( $N + 1 ))
+  N=$(( N + 1 ))
 done
 
 if [ $N -gt 0 ]; then

line.sh

@@ -1,5 +1,5 @@
 #!/bin/bash --noprofile
-THIS=`dirname $0`
+THIS=$( dirname $0 )
 source $THIS/bash_common.sh
 if [ $# -ne 2 ]; then
   echo "#1: File name"
@@ -10,7 +10,7 @@ F=$1
 L=$2
 
 
-N=`cat $F | wc -l`
+N=$( cat $F | wc -l )
 if [ $L -gt $N ]; then
   error "Max. line = $N"
 fi

make.sh

@@ -3,7 +3,7 @@
 
 unset AT_NCBI
 
-cd `dirname $0`
+cd "$( dirname $0 )"
 source ./bash_common.sh
 export CPP_DIR=$PWD
 

parent_dir.sh

@@ -1,5 +1,5 @@
 #!/bin/bash --noprofile
-THIS=`dirname $0`
+THIS=$( dirname $0 )
 source $THIS/bash_common.sh
 if [ $# -ne 1 ]; then
   echo "Print parent directory"
@@ -8,6 +8,6 @@ fi
 F=$1
 
 
-D=`dirname $F`
-P=`realpath $D`
+D=$( dirname $F )
+P=$( realpath $D )
 basename $P

phylogeny/distTree_inc.sh

@@ -74,7 +74,7 @@ if true; then
   fi
 
 
-  VER=$(( $VER + 1 ))
+  VER=$(( VER + 1 ))
   echo $VER > $INC/version
 
   THREADS=$( file2var $INC/threads 15 )

qstat_wait.sh

@@ -1,5 +1,5 @@
 #!/bin/bash --noprofile
-THIS=`dirname $0`
+THIS=$( dirname $0 )
 source $THIS/bash_common.sh
 if [ $# -ne 2 ]; then
   echo "#1: seconds to wait after all jobs are in 'r' state. 0: resubmit and stop"
@@ -14,14 +14,14 @@ comment "Waiting for UGE results"
 
 
 SLEEP_SEC=10  # PAR
-PERIODS=$(( $SECS / $SLEEP_SEC ))
+PERIODS=$(( SECS / SLEEP_SEC ))
 
 
 while true; do
   sleep $SLEEP_SEC
   $THIS/grid_wait.sh 0
   set +o errexit
-  Q=`qstat | grep -v '^job-ID' | grep -v '^---' | grep '   qw   ' | wc -l`
+  Q=$( qstat | grep -v '^job-ID' | grep -v '^---' | grep -c '   qw   ' )
   set -o errexit
   if [ $Q == 0 ]; then
     break
@@ -34,18 +34,18 @@ while true; do
   sleep $SLEEP_SEC
   $THIS/grid_wait.sh 0
   set +o errexit
-  Q=`qstat | grep -v '^job-ID' | grep -v '^---' | grep -v '   d[tr]   ' | wc -l`
+  Q=$( qstat | grep -v '^job-ID' | grep -v '^---' | grep -vc '   d[tr]   ' )
   set -o errexit
   if [ $Q == 0 ]; then
     break
   fi
 
-  N=$(( $N + 1 ))
+  N=$(( N + 1 ))
   if [ $N -gt $PERIODS ]; then  
     N=0
     $THIS/grid_wait.sh 1
     set +o errexit
-    L=(`qstat | grep -v '^job-ID' | grep -v '^---' | grep -v '   d[tr]   ' | grep '  [rTt]  ' | sed 's/^ *//1' | cut -f 1 -d ' '`)
+    L=( $( qstat | grep -v '^job-ID' | grep -v '^---' | grep -v '   d[tr]   ' | grep '  [rTt]  ' | sed 's/^ *//1' | cut -f 1 -d ' ' ) )
     set -o errexit
     M=${#L[@]}
     if [ $M -ne 0 ]; then 
@@ -56,13 +56,13 @@ while true; do
         while [ $i -lt $M ]; do
           $THIS/grid_wait.sh 1
   	      qresub ${L[$i]} -h u || true
-  	      i=$(($i + 1))
+  	      i=$(( i + 1 ))
         done
       else
         warning "Deleting $M UGE jobs"
       fi
       $THIS/grid_wait.sh 1
-      qdel -f ${L[@]} || true
+      qdel -f "${L[@]}" || true
       if [ $QRESUB == 1 ]; then
         $THIS/grid_wait.sh 1
         qrls  -h u  -u $USER > /dev/null

rmBOM.sh

@@ -1,5 +1,5 @@
 #!/bin/bash --noprofile
-THIS=`dirname $0`
+THIS=$( dirname $0 )
 source $THIS/bash_common.sh
 if [ $# -ne 2 ]; then
   echo "Remove UTF-8 Byte Order Mark"

rm_all.sh

@@ -1,5 +1,5 @@
 #!/bin/bash --noprofile
-THIS=`dirname $0`
+THIS=$( dirname $0 )
 source $THIS/bash_common.sh
 if [ $# -ne 1 ]; then
   echo "Delete #1 without 'rm -r' which is slow"
@@ -14,7 +14,7 @@ if [ ! -e "$DIR" ]; then
 fi
 
 
-TMP=`mktemp -d`
+TMP=$( mktemp -d )
 
 rsync -a --delete $TMP/ "$DIR"
 rmdir "$DIR"

rm_suff.sh

@@ -1,5 +1,5 @@
 #!/bin/bash --noprofile
-THIS=`dirname $0`
+THIS=$( dirname $0 )
 source $THIS/bash_common.sh
 if [ $# -ne 2 ]; then
   echo "Remove a suffix from a file name"
@@ -11,8 +11,8 @@ FILE=$1
 SUF=$2
 
 
-DIR=`dirname $FILE`
-OUT=`basename $FILE $SUF`
+DIR=$( dirname $FILE )
+OUT=$( basename $FILE $SUF )
 if [ "$FILE" != "$DIR/$OUT" ]; then
   mv $FILE $DIR/$OUT
 fi

setIntersect.sh

@@ -1,5 +1,5 @@
 #!/bin/bash --noprofile
-THIS=`dirname $0`
+THIS=$( dirname $0 )
 source $THIS/bash_common.sh
 if [ $# -ne 3 ]; then
   echo "#1: List1"
@@ -18,7 +18,7 @@ if [ $NUMP == 1 ]; then
   NUM="-number"
 fi
 
-TMP=`mktemp` 
+TMP=$( mktemp )
 #comment $TMP
 #set -x
 

sort.sh

@@ -1,11 +1,11 @@
 #!/bin/bash --noprofile
-THIS=`dirname $0`
+THIS=$( dirname $0 )
 source $THIS/bash_common.sh
 if [ $# -ne 1 ]; then
   echo "#1: File to sort"
   exit 1
 fi
 
-TMP=`mktemp`
+TMP=$( mktemp )
 sort $1 > $TMP
 mv $TMP $1

tar.sh

@@ -1,5 +1,5 @@
 #!/bin/bash --noprofile
-THIS=`dirname $0`
+THIS=$( dirname $0 )
 source $THIS/bash_common.sh
 if [ $# -ne 2 ]; then
   echo "tar #1/ into #.tar.gz"

test.sh

@@ -1,5 +1,5 @@
 #!/bin/bash --noprofile
-THIS=$( realpath $( dirname $0 ) )
+THIS=$( realpath "$( dirname $0 )" )
 source $THIS/bash_common.sh
 
 

uniq.sh

@@ -1,12 +1,12 @@
 #!/bin/bash --noprofile
-THIS=`dirname $0`
+THIS=$( dirname $0 )
 source $THIS/bash_common.sh
 if [ $# != 1 ]; then
   echo "#1: File to sort and uniq"
   exit 1
 fi
 
-TMP=`mktemp`
+TMP=$( mktemp )
 cat $1 | tr '\t' ' ' | sed 's/ *$//1' | sed 's/  / /g' | sort -u | tr ' ' '\t' > $TMP
 mv $TMP $1