fix error if folder exists

mjoppich · May 17, 2019 · fdb3548 · fdb3548
1 parent 3b492e9
commit fdb3548
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Showing 6 changed files with 23 additions and 8 deletions.
diff --git a/install_templates/install_bowtie1.igui b/install_templates/install_bowtie1.igui
@@ -43,12 +43,13 @@ mkdir -p "$PROGDIR"
 #download and unzip
 wget https://sourceforge.net/projects/bowtie-bio/files/bowtie/1.1.2/bowtie-1.1.2-src.zip/download -O "$PROGDIR/$PROG.zip"
 
+if [ -d "$PROGDIR/$PROG" ]; then
+    echo "Removing Folder $PROGDIR/$PROG"
+    rm -rf "$PROGDIR/$PROG"
+fi
 
-
-if [ ! -d "$PROGDIR/$PROG" ]; then
 unzip -d "$PROGDIR/$PROG" "$PROGDIR/$PROG.zip"
 mv "$PROGDIR/$PROG/"*/* "$PROGDIR/$PROG"
-fi
 
 cd "$PROGDIR/$PROG"
 

diff --git a/install_templates/install_bowtie2.igui b/install_templates/install_bowtie2.igui
@@ -41,7 +41,11 @@ fi
 ## create progdir
 mkdir -p "$PROGDIR"
 
-rm -rf ${PROGDIR}/${PROG}/
+
+if [ -d "$PROGDIR/$PROG" ]; then
+    echo "Removing Folder $PROGDIR/$PROG"
+    rm -rf "$PROGDIR/$PROG"
+fi
 
 #download and unzip
 wget https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.3.4.3/bowtie2-2.3.4.3-source.zip/download -O "$PROGDIR/$PROG.zip"

diff --git a/install_templates/install_bwa.igui b/install_templates/install_bwa.igui
@@ -40,8 +40,9 @@ fi
 ## create progdir
 mkdir -p "$PROGDIR/"
 
-if [-z ${PROGDIR}/${PROG} ]; then
-    rm -rf ${PROGDIR}/${PROG}
+if [ -d "$PROGDIR/$PROG" ]; then
+    echo "Removing Folder $PROGDIR/$PROG"
+    rm -rf "$PROGDIR/$PROG"
 fi
 
 #download and unzip

diff --git a/install_templates/install_canu.igui b/install_templates/install_canu.igui
@@ -45,7 +45,7 @@ fi
 
 if [ -d "$PROGDIR/$PROG" ]; then
     echo "Removing Folder $PROGDIR/$PROG"
-    rm -rf $PROGDIR/$PROG
+    rm -rf "$PROGDIR/$PROG"
 fi
 
 ## create progdir

diff --git a/install_templates/install_glimmer.igui b/install_templates/install_glimmer.igui
@@ -36,6 +36,11 @@ echo "PROGDIRESC $PROGDIRESC"
 
 APPBINARYDIR="${PROGDIRESC}/${PROG}/"
 
+if [ -d "$PROGDIR/$PROG" ]; then
+    echo "Removing Folder $PROGDIR/$PROG"
+    rm -rf "$PROGDIR/$PROG"
+fi
+
 ## create progdir
 mkdir -p "$PROGDIR/$PROG"
 

diff --git a/install_templates/install_hisat.igui b/install_templates/install_hisat.igui
@@ -41,10 +41,14 @@ fi
 
 PROGDIRESC=$(echo $PROGDIR | sed 's/ /\\ /g')
 
-
 ## create progdir
 mkdir -p "$PROGDIR"
 
+if [ -d "$PROGDIR/$PROG" ]; then
+    echo "Removing Folder $PROGDIR/$PROG"
+    rm -rf "$PROGDIR/$PROG"
+fi
+
 #download and unzip
 cd "$PROGDIR"
 git clone https://github.com/infphilo/hisat2.git $PROG