fix templates to run on mac.

mjoppich · Jan 7, 2019 · 567807e · 567807e
1 parent 20f112c
commit 567807e
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Showing 7 changed files with 92 additions and 60 deletions.
diff --git a/install_templates/install_hisat.igui b/install_templates/install_hisat.igui
@@ -1,17 +1,24 @@
 #! Install hisat2-2.0.5
 
-echo "Dependencies: unzip"
 if [ ! "$2" = "" ]; then
-	echo "Installing dependencies"
-	echo $2 | sudo -S apt-get update
-	echo $2 | sudo -S apt-get -y install unzip
-
+
+    if [ "$(uname)" == "Darwin" ]; then
+
+        echo "Installing brew gcc"
+        brew install gcc
+
+    else
+
+        echo "No dependencies"
+
+    fi
+
 else
-	echo "No sudo password, not installing dependencies"
+   echo "No sudo password, not installing dependencies"
 fi
 
 ## set all variables
-PROG=hisat2-2.0.5
+PROG=hisat2-2.1.0
 
 PROGDIR=$1
 if [ -z "${PROGDIR}" ]; then
@@ -25,16 +32,8 @@ PROGDIRESC=$(echo $PROGDIR | sed 's/ /\\ /g')
 mkdir -p "$PROGDIR"
 
 #download and unzip
-if [ ! -f "$PROGDIR/$PROG.zip" ]; then
-	wget ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/downloads/hisat2-2.0.5-source.zip -O "$PROGDIR/$PROG.zip"
-fi
-
-if [ ! -d "$PROGDIR/$PROG" ]; then
 cd "$PROGDIR"
-
-
-unzip $PROG.zip -d "$PROGDIR/"
-fi
+git clone https://github.com/infphilo/hisat2.git $PROG
 
 #install prog
 cd "$PROGDIR/$PROG"
@@ -72,8 +71,8 @@ fi
 
 $NCCMD <<EOF
 
-<template description="hisat2 2.0.5 aligner" title="hisat2 2.0.5">
-<window title="hisat2 2.0.5 aligner">
+<template description="hisat2 2.1.0 aligner" title="hisat2 2.1.0">
+<window title="hisat2 2.1.0 aligner">
 <vgroup>
 
   <group title="Alignment Information">

diff --git a/install_templates/install_hmmer.igui b/install_templates/install_hmmer.igui
@@ -30,7 +30,7 @@ fi
 #install prog
 cd "$PROGDIR/$PROG"
 
-./configure# -prefix="$PROGDIR/$PROG"
+./configure #-prefix="$PROGDIR/$PROG"
 make
 #make check
 # does not really work on mac os

diff --git a/install_templates/install_rmats.igui b/install_templates/install_rmats.igui
@@ -1,17 +1,28 @@
 #! Install rMATS-3.2.5
 
+
+
+if [ "$(uname)" == "Darwin" ]; then
+
+	echo "This Install Module is not compatible with Mac OS. If desperately needed, contact bioGUI authors."
+	exit
+fi
+
+
 echo "Dependencies: python2.7 python-pip zlib1g-dev numpy scipy pysam"
+
 if [ ! "$2" = "" ]; then
+
 	echo "Installing dependencies"
 	echo $2 | sudo -S apt-get update
 	echo $2 | sudo -S apt-get -y install python2.7 python-pip zlib1g-dev
-
-	pip install numpy scipy pysam
-
+
 else
-	echo "No sudo password, not installing dependencies"
+   echo "No sudo password, not installing dependencies"
 fi
 
+pip install numpy scipy pysam
+
 ## set all variables
 PROG=rMATS.3.2.5
 PROGNICE=rMATS-3.2.5
@@ -27,9 +38,7 @@ PROGDIRESC=$(echo $PROGDIR | sed 's/ /\\ /g')
 mkdir -p "$PROGDIR"
 
 #download and unzip
-if [ ! -f "$PROGDIR/$PROG.tgz" ]; then
-	wget https://sourceforge.net/projects/rnaseq-mats/files/MATS/rMATS.3.2.5.tgz/download -O "$PROGDIR/$PROG.tgz"
-fi
+wget https://sourceforge.net/projects/rnaseq-mats/files/MATS/rMATS.3.2.5.tgz/download -O "$PROGDIR/$PROG.tgz"
 
 
 if [ ! -d "$PROGDIR/$PROG" ]; then

diff --git a/install_templates/install_rsem.igui b/install_templates/install_rsem.igui
@@ -1,5 +1,11 @@
 #! Install RSEM 1.3.0
 
+if [ "$(uname)" == "Darwin" ]; then
+
+	echo "This Install Module is not compatible with Mac OS. If desperately needed, contact bioGUI authors."
+	exit
+fi
+
 echo "Dependencies: perl r-base python numpy scipy pysam"
 if [ ! "$2" = "" ]; then
 	echo "Installing dependencies"

diff --git a/install_templates/install_samtools.igui b/install_templates/install_samtools.igui
@@ -1,12 +1,22 @@
 #! Install samtools-1.3.1
 
-echo "Dependencies: libncurses5-dev"
+
 if [ ! "$2" = "" ]; then
-	echo "Installing dependencies"
-	echo $2 | sudo -S apt-get update
-	echo $2 | sudo -S apt-get -y install libncurses5-dev zlib1g-dev
+
+    if [ "$(uname)" == "Darwin" ]; then
+
+        echo "Installing brew gcc"
+        brew install gcc zlib 
+
+    else
+
+		echo "Installing dependencies"
+		echo $2 | sudo -S apt-get update
+		echo $2 | sudo -S apt-get -y install libncurses5-dev zlib1g-dev
+    fi
+
 else
-	echo "No sudo password, not installing dependencies"
+   echo "No sudo password, not installing dependencies"
 fi
 
 ## set all variables

diff --git a/install_templates/install_stringtie.igui b/install_templates/install_stringtie.igui
@@ -2,19 +2,28 @@
 
 echo "Dependencies: perl r-base python 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
+
+        alias gcc='gcc-8'
+        alias g++='g++-8'
+
+    else
+
+        echo "No dependencies"
+
+    fi
+
 else
-	echo "No sudo password, not installing dependencies"
+   echo "No sudo password, not installing dependencies"
 fi
 
 ## set all variables
-PROG=StringTie_1_3_0
-PROGNICE=StringTie1.3.0
+PROG=StringTie_1_3_5
+PROGNICE=StringTie1.3.5
 PROGDIR=$1
 
 if [ -z "${PROGDIR}" ]; then
@@ -28,16 +37,11 @@ APPBINARYDIR=${PROGDIR}/${PROG}/
 mkdir -p "$PROGDIR"
 
 #download and unzip
-if [ ! -f "$PROGDIR/$PROG.tar.gz" ]; then
-	wget http://ccb.jhu.edu/software/stringtie/dl/stringtie-1.3.0.tar.gz -O "$PROGDIR/$PROG.tar.gz"
-fi
+wget http://ccb.jhu.edu/software/stringtie/dl/stringtie-1.3.5.tar.gz -O "$PROGDIR/$PROG.tar.gz"
 
-
-if [ ! -d "$PROGDIR/$PROG" ]; then
-	tar xvfz "$PROGDIR/$PROG.tar.gz" -C "$PROGDIR"
-	cd "$PROGDIR"
-	mv stringtie-1.3.0 $PROG
-fi
+tar xvfz "$PROGDIR/$PROG.tar.gz" -C "$PROGDIR"
+cd "$PROGDIR"
+mv stringtie-1.3.5 $PROG
 
 cd "$PROGDIR/$PROG"
 

diff --git a/install_templates/install_trimmomatic.igui b/install_templates/install_trimmomatic.igui
@@ -1,12 +1,20 @@
 #! Install Trimmomatic 0.36
 
-echo "Dependencies: java (openjdk)"
 if [ ! "$2" = "" ]; then
-	echo "Installing dependencies"
-	echo $2 | sudo -S apt-get update
-	echo $2 | sudo -S apt-get -y install openjdk-9-jre
+
+    if [ "$(uname)" == "Darwin" ]; then
+
+        echo "PLEASE INSTALL JAVA PRIOR USING TRIMMOMATIC!"
+
+    else
+
+		echo "Installing dependencies: openjdk 9"
+		echo $2 | sudo -S apt-get update
+		echo $2 | sudo -S apt-get -y install openjdk-9-jre
+    fi
+
 else
-	echo "No sudo password, not installing dependencies"
+   echo "No sudo password, not installing dependencies"
 fi
 
 ## set all variables
@@ -27,15 +35,11 @@ echo "Creating $PROGDIR"
 mkdir -p "$PROGDIR"
 
 #download and unzip
-if [ ! -f "$PROGDIR/$PROG.zip" ]; then
-echo "Downloading program"
-	wget http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/$PROGNICE.zip -O "$PROGDIR/$PROG.zip"
-fi
+echo "Downloading Trimmomatic"
+wget http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/$PROGNICE.zip -O "$PROGDIR/$PROG.zip"
 
-if [ ! -d "$PROGDIR/$PROG" ]; then
 unzip -o "$PROGDIR/$PROG.zip" -d "$PROGDIR/$PROG"
 mv "$PROGDIR/$PROG/"*/* "$PROGDIR/$PROG"
-fi
 
 if [ $# -gt 2 ]; then