improved export of MYSMISDIR

wtsi-hpag · Sep 22, 2017 · 625bcb1 · 625bcb1
1 parent 85fff4c
commit 625bcb1
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Showing 3 changed files with 11 additions and 5 deletions.
diff --git a/makeall.sh b/makeall.sh
@@ -3,18 +3,24 @@
 errs=0
 MYSMISDIR=`pwd`
 
+
+sed -i '/export/d' src/makefile 
+sed -i '/export MYSMISDIR/d' setup.sh 
+
+
+
 setdone=`grep "export MYSMISDIR" setup.sh | wc -l`
 if [[ $setdone < 2 ]]; then 
     setsmis=`echo export MYSMISDIR=$MYSMISDIR` 
-    sed -i '5i\'"$setsmis" setup.sh
+    sed -i '2i\'"$setsmis" setup.sh
 fi
 
 export MYSMISDIR=$MYSMISDIR
 setdone=0
 setdone=`grep "export MYSMISDIR" src/makefile  | wc -l`
 if [[ $setdone < 1 ]]; then
     setsmis=`echo export MYSMISDIR=$MYSMISDIR`
-    sed -i '3i\'"$setsmis" src/makefile 
+    sed -i '1i\'"$setsmis" src/makefile 
 fi
 
 

diff --git a/setup.sh b/setup.sh
@@ -1,7 +1,6 @@
 #!/bin/bash
 
 
-
 odir=$1    
 fafile=$2
 fqfile=$3
@@ -21,7 +20,7 @@ mkdir -p $odir
 cd $odir
 
 rm -f mysettings.sh
-echo "export MYSMISDIR="$MYSMISDIR > mysettings.sh
+echo export "MYSMISDIR="$MYSMISDIR > mysettings.sh
 sed -e "s#ODIR#$odir#g"  $MYSMISDIR/settings.sh \
 	| sed -e "s#FAFILE#$fafile#g" | sed -e "s#FQFILE#$fqfile#g"   >> mysettings.sh
 

diff --git a/src/makefile b/src/makefile
@@ -1,4 +1,5 @@
-# Makefile for smis_scaffold 
+
+
 CC=c++
Original file line number	Diff line number	Diff line change
		@@ -1,4 +1,5 @@
		# Makefile for smis_scaffold


		CC=c++


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