fix bowties mac

install_templates/install_bowtie1.igui

@@ -1,16 +1,28 @@
 #! Install Bowtie1
 
-echo "Dependencies: perl, python, r-base, numpy, scipy, pysam"
+
 if [ ! "$2" = "" ]; then
-	echo "Installing dependencies"
-	echo $2 | sudo -S apt-get update
-	echo $2 | sudo -S apt-get -y install perl r-base python
-
-	pip install numpy scipy pysam
+
+    if [ "$(uname)" == "Darwin" ]; then
+
+        echo "Installing brew gcc"
+        brew install gcc
+
+
+    else
+
+		echo "Installing dependencies"
+		echo $2 | sudo -S apt-get update
+		echo $2 | sudo -S apt-get -y install python
+
+		pip install numpy scipy pysam
+    fi
+
 else
-	echo "No sudo password, not installing dependencies"
+   echo "No sudo password, not installing dependencies"
 fi
 
+
 ## set all variables
 PROG=bowtie_1_1_2
 PROGNICE=Bowtie-1.1.2
@@ -21,15 +33,14 @@ if [ -z "${PROGDIR}" ]; then
 fi
 
 PROGDIRESC=$(echo $PROGDIR | sed 's/ /\\ /g')
-APPBINARYDIR=${PROGDIRESC}/${PROG}/
+APPBINARYDIR=${PROGDIR}/${PROG}/
 
 ## create progdir
 mkdir -p "$PROGDIR"
 
 #download and unzip
-if [ ! -f "$PROGDIR/$PROG.zip" ]; then
-	wget https://sourceforge.net/projects/bowtie-bio/files/bowtie/1.1.2/bowtie-1.1.2-src.zip/download -O "$PROGDIR/$PROG.zip"
-fi
+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

install_templates/install_bowtie2.igui

@@ -1,23 +1,32 @@
 #! Install Bowtie2 2.2.9
 
-echo "Dependencies: perl, python, r-base, numpy, scipy, pysam"
 if [ ! "$2" = "" ]; then
-	echo "Installing dependencies"
-	echo $2 | sudo -S apt-get update
-	echo $2 | sudo -S apt-get -y install perl r-base python
-
-	pip install numpy scipy pysam
+
+    if [ "$(uname)" == "Darwin" ]; then
+
+        echo "Installing brew gcc tbb"
+        brew install gcc tbb
+
+
+    else
+
+		echo "Installing dependencies"
+		echo $2 | sudo -S apt-get update
+		echo $2 | sudo -S apt-get -y install libtbb-dev
+
+    fi
+
 else
-	echo "No sudo password, not installing dependencies"
+   echo "No sudo password, not installing dependencies"
 fi
 
 ## set all variables
-PROG=bowtie2_2_2_9
-PROGNICE=Bowtie2-2.2.9
+PROG=bowtie2_2_3_4_3
+PROGNICE=Bowtie2-2.3.4.3
 PROGDIR=$1
 
 PROGDIRESC=$(echo $PROGDIR | sed 's/ /\\ /g')
-APPBINARYDIR=${PROGDIRESC}/${PROG}/
+APPBINARYDIR=${PROGDIR}/${PROG}/
 
 if [ -z "${PROGDIR}" ]; then
 	PROGDIR=~/bioGUI/progs/
@@ -27,19 +36,18 @@ fi
 mkdir -p "$PROGDIR"
 
 #download and unzip
-if [ ! -f "$PROGDIR/$PROG.zip" ]; then
-	wget https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.2.9/bowtie2-2.2.9-source.zip/download -O "$PROGDIR/$PROG.zip"
-fi
-
+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"
 
-if [ ! -d "$PROGDIR/$PROG" ]; then
 unzip -d "$PROGDIR/$PROG" "$PROGDIR/$PROG.zip"
 mv "$PROGDIR/$PROG/"*/* "$PROGDIR/$PROG"
-fi
 
 cd "$PROGDIR/$PROG"
 
-make
+if [ "$(uname)" == "Darwin" ]; then
+	make CC=gcc-8 CPP=g++-8
+else
+	make
+fi
 
 if [ $# -gt 2 ]; then