fix ballgown install

mjoppich · May 15, 2019 · 71cf890 · 71cf890
2 parents aef0009 + 62e50ba
commit 71cf890
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Showing 21 changed files with 222 additions and 84 deletions.
diff --git a/install_templates/install_apple_first.igui b/install_templates/install_apple_first.igui
@@ -4,31 +4,37 @@ echo "First Time Mac OS Setup"
 
 if [ "$(uname)" == "Darwin" ]; then
 
-	echo "Dependencies: pip "
+	echo "Installing Dependencies"
+
 	if [ ! "$2" = "" ]; then
 
-		HASPORTS=`which port`
-		if [ -z "$HASPORTS" ]
-		then
-			(>&2 echo "PLEASE INSTALL MACPORTS FIRST")
-			(>&2 echo "YOU CAN DOWNLOAD MACPORTS FROM")
+		source ~/.bashrc
+		source ~/.bash_profile
+
+		HASBREW=`which brew`
+
+		if [ -z "$HASBREW" ]; then
+
+			(>&2 echo "PLEASE INSTALL homebrew FIRST")
+			(>&2 echo "YOU CAN DOWNLOAD homebrew FROM")
 			(>&2 echo "")
-			(>&2 echo "https://www.macports.org/")
+			(>&2 echo "https://brew.sh")
 			(>&2 echo "")
+			(>&2 echo "If you installed homebrew and this warning persists run brew doctor")
+			(>&2 echo "and add brew to your PATH: echo \'export PATH=\"/usr/local/bin:\$PATH\"\' >> ~/.bash_profile")
 		else
+			echo "Installing dependencies: gcc@8, pip, python3, pip3"
+
+			echo $2 | sudo -S mkdir -p /usr/local/lib 
+			echo $2 | sudo -S mkdir -p /usr/local/Frameworks
 
-		echo "Installing dependencies: Mac pip, python36, pip36 as python3 and pip3"
-		echo $2 | sudo -S easy_install pip
-
-		echo $2 | sudo -S port -N install python36 
-		echo $2 | sudo port select --set python3 python36
-
-		echo $2 | sudo -S port -N install py36-pip
-		echo $2 | sudo -S port select --set pip3 pip36
+			echo $2 |sudo chown -R $(whoami) $(brew --prefix)/*
+			brew install gcc@8 python3
 
-		echo $2 | sudo -S port -N install wget gcc8
+			curl https://bootstrap.pypa.io/get-pip.py -o /tmp/get-pip.py
+			python3 /tmp/get-pip.py
 
-		echo "Enjoy bioGUI!"
+			echo "Enjoy bioGUI!"
 
 		fi
 

diff --git a/install_templates/install_ballgown.igui b/install_templates/install_ballgown.igui
@@ -13,7 +13,7 @@ if [ ! "$2" = "" ]; then
 
         echo "Dependencies: $DEP_PACKAGES R: devtools, RSkittleBrewer, ballgown"
         echo $2 | sudo -S apt-get update
-        echo $2 | sudo -S apt-get install $DEP_PACKAGES
+        echo $2 | sudo -S apt-get -y install r-base zlibc zlib1g zlib1g-dev libxml2-dev libcurl4-openssl-dev
 
     fi
 
@@ -26,7 +26,7 @@ echo "options(repos = c(CRAN = \"https://cran.rstudio.com\"))" > ~/.Rprofile
 RLIBSUSER=`Rscript -e "cat(Sys.getenv('R_LIBS_USER'))"`
 mkdir -p $RLIBUSER
 
-Rscript -e "source(\"http://bioconductor.org/biocLite.R\"); install.packages(\"devtools\"); devtools::install_github('alyssafrazee/RSkittleBrewer'); biocLite(\"ballgown\", lib.loc=Sys.getenv('R_LIBS_USER'), lib=Sys.getenv('R_LIBS_USER'));"
+Rscript -e "source(\"http://bioconductor.org/biocLite.R\"); install.packages(\"devtools\"); install.packages(\"dplyr\"); devtools::install_github('alyssafrazee/RSkittleBrewer'); biocLite(\"ballgown\", lib.loc=Sys.getenv('R_LIBS_USER'), lib=Sys.getenv('R_LIBS_USER'));"
 
 RSCRIPT=`which Rscript`
 

diff --git a/install_templates/install_bowtie1.igui b/install_templates/install_bowtie1.igui
@@ -1,22 +1,24 @@
 #! Install Bowtie1
 
+if [ "$(uname)" == "Darwin" ]; then
+	source ~/.bash_profile
+else
+  echo ""
+fi
 
 if [ ! "$2" = "" ]; then
 
     if [ "$(uname)" == "Darwin" ]; then
 
-        echo "Installing brew gcc"
-        brew install gcc
-
+        echo "bowtie1 install module is not compatible with Mac OS. Use bowtie2"
+        exit;
 
     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
+      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"
@@ -64,7 +66,7 @@ if [ $# -gt 2 ]; then
 fi
 
 APPBINARYESC="${PROGDIRESC}/${PROG}/"
-APPBINARY="${PROGDIRESC}/${PROG}/bowtie"
+APPBINARY="${PROGDIRESC}/${PROG}/bowtie-align-s"
 if [ -z "$(ls -A ${APPBINARYESC})" ] || [ ! -f ${APPBINARY} ]; then
    (>&2 echo ${APPBINARYESC})
    (>&2 ls ${APPBINARYESC})

diff --git a/install_templates/install_bowtie2.igui b/install_templates/install_bowtie2.igui
@@ -1,14 +1,17 @@
 #! Install Bowtie2 2.2.9
 
+if [ "$(uname)" == "Darwin" ]; then
+	source ~/.bash_profile
+else
+  echo ""
+fi
+
 if [ ! "$2" = "" ]; then
 
     if [ "$(uname)" == "Darwin" ]; then
 
-      echo "Installing brew gcc tbb"
-      brew install gcc tbb
-
-      alias gcc='gcc-8'
-      alias g++='g++-8'
+        echo "Installing brew wget gcc@8 tbb"
+        brew install wget gcc@8 tbb
 
 
     else
@@ -38,6 +41,8 @@ fi
 ## create progdir
 mkdir -p "$PROGDIR"
 
+rm -rf ${PROGDIR}/${PROG}/
+
 #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"
 
@@ -65,7 +70,7 @@ fi
 
 
 APPBINARYESC="${PROGDIRESC}/${PROG}/"
-APPBINARY="${PROGDIRESC}/${PROG}/bowtie2"
+APPBINARY="${PROGDIRESC}/${PROG}/bowtie2-align-s"
 if [ -z "$(ls -A ${APPBINARYESC})" ] || [ ! -f ${APPBINARY} ]; then
    (>&2 echo ${APPBINARYESC})
    (>&2 ls ${APPBINARYESC})

diff --git a/install_templates/install_bwa.igui b/install_templates/install_bwa.igui
@@ -1,11 +1,17 @@
 #! Install bwa 0.7.17 (sourceforge)
 
+if [ "$(uname)" == "Darwin" ]; then
+	source ~/.bash_profile
+else
+  echo ""
+fi
+
 if [ ! "$2" = "" ]; then
 
     if [ "$(uname)" == "Darwin" ]; then
 
-        echo "Installing brew gcc tbb"
-        brew install gcc tbb
+        echo "Installing brew gcc@8"
+        brew install gcc@8
 
     else
 

diff --git a/install_templates/install_featurecounts.igui b/install_templates/install_featurecounts.igui
@@ -1,16 +1,17 @@
 #! Install featureCounts (github)
 
-
+if [ "$(uname)" == "Darwin" ]; then
+	source ~/.bash_profile
+else
+  echo ""
+fi
 
 if [ ! "$2" = "" ]; then
 
     if [ "$(uname)" == "Darwin" ]; then
 
         echo "Installing brew gcc"
-        brew install gcc
-
-        alias gcc='gcc-8'
-        alias g++='g++-8'
+        brew install gcc@8
 
     else
 
@@ -57,7 +58,13 @@ mv */* .
 cd "$PROGDIR/$PROG/src"
 
 if [ "$(uname)" == "Darwin" ]; then
-	make -f Makefile.MacOS
+    echo "Compile MAC OS"
+
+    echo "Modifying Makefile.MacOS"
+    sed -i '' 's/CC \= gcc/CC \= \$\{GCC\}/g' Makefile.MacOS
+
+    echo "Compiling subread"
+    LDFLAGS="-L/usr/local/lib" CPPFLAGS="-I/usr/local/include/" make -f Makefile.MacOS GCC=gcc-8 CC_EXEC=gcc-8
 else
 	make -f Makefile.Linux
 fi

diff --git a/install_templates/install_graphmap.igui b/install_templates/install_graphmap.igui
@@ -1,13 +1,17 @@
 #! Install graphmap (github))
 
-
+if [ "$(uname)" == "Darwin" ]; then
+	source ~/.bash_profile
+else
+  echo ""
+fi
 
 if [ ! "$2" = "" ]; then
 
     if [ "$(uname)" == "Darwin" ]; then
 
         echo "Installing brew gcc"
-        brew install gcc
+        brew install gcc@8
 
         alias gcc='gcc-8'
         alias g++='g++-8'

diff --git a/install_templates/install_hisat.igui b/install_templates/install_hisat.igui
@@ -1,11 +1,21 @@
 #! Install hisat2 (github)
 
+if [ "$(uname)" == "Darwin" ]; then
+	source ~/.bash_profile
+else
+  echo ""
+fi
+
 if [ ! "$2" = "" ]; then
 
     if [ "$(uname)" == "Darwin" ]; then
 
-        echo "Installing brew gcc"
-        brew install gcc
+        echo "Installing brew gcc gawk"
+        echo "Installing gawk only for libmpfr.4.dylib ..."
+        brew install gcc@8 gawk
+
+        alias gcc='gcc-8'
+        alias g++='g++-8'
 
         alias gcc='gcc-8'
         alias g++='g++-8'
@@ -106,8 +116,8 @@ fi
 
 $NCCMD <<EOF
 
-<template description="hisat2 2.1.0 aligner" title="hisat2 2.1.0">
-<window title="hisat2 2.1.0 aligner">
+<template description="hisat2 aligner (github)" title="hisat2 (github)">
+<window title="hisat2 aligner (github)">
 <vgroup>
 
   <group title="Alignment Information">

diff --git a/install_templates/install_mm_asm_racon.igui b/install_templates/install_mm_asm_racon.igui
@@ -1,11 +1,17 @@
 #! Install minimap2/miniasm/racon (github)
 
+if [ "$(uname)" == "Darwin" ]; then
+	source ~/.bash_profile
+else
+  echo ""
+fi
+
 if [ ! "$2" = "" ]; then
 
     if [ "$(uname)" == "Darwin" ]; then
 
         echo "Installing Dependencies (mac)"
-        brew install cmake gcc
+        brew install cmake gcc@8
     else
 
         echo "Installing Dependencies (aptitude/Ubuntu)"
@@ -41,11 +47,23 @@ mkdir -p "$PROGDIR/$PROG"
 
 cd "$PROGDIR/$PROG"
 git clone https://github.com/lh3/minimap2 minimap2
-cd minimap2 && make
+cd minimap2
+
+if [ "$(uname)" == "Darwin" ]; then
+	make CC=gcc-8
+else
+	make
+fi
 
 cd "$PROGDIR/$PROG"
 git clone https://github.com/lh3/miniasm miniasm
-cd miniasm  && make
+cd miniasm
+
+if [ "$(uname)" == "Darwin" ]; then
+	make CC=gcc-8
+else
+	make
+fi
 
 cd "$PROGDIR/$PROG"
 git clone --recursive https://github.com/isovic/racon.git racon

diff --git a/install_templates/install_msempire.igui b/install_templates/install_msempire.igui
@@ -1,19 +1,25 @@
 #! Install ms-EmpiRe
 
 if [ "$(uname)" == "Darwin" ]; then
-
-	echo "This Install Module is not compatible with Mac OS. If desperately needed, contact bioGUI authors."
-	exit
+	source ~/.bash_profile
+else
+  echo ""
 fi
 
 echo "Dependencies: r-base"
 if [ ! "$2" = "" ]; then
 
     if [ "$(uname)" == "Darwin" ]; then
 
-        echo "Installing R"
+        echo "Installing R and setting PATH for R libraries"
+        brew install gcc
+        brew link --overwrite gcc
+        brew install openblas
+        brew install libgit2 libxml2 openssl
         brew install r
 
+        CC=clang CXX=clang++ Rscript -e 'install.packages("git2r", repos="https://cran.cnr.berkeley.edu/")'
+
     else
 
         echo "Installing dependencies"
@@ -39,14 +45,18 @@ fi
 PROGDIRESC=$(echo $PROGDIR | sed 's/ /\\ /g')
 APPBINARYDIR="${PROGDIR}/${PROG}/"
 
+rm -rf "$PROGDIR/$PROG"
 
 ## create progdir
 mkdir -p "$PROGDIR/$PROG"
 
 cd "$PROGDIR/$PROG"
 
-wget https://gist.githubusercontent.com/mjoppich/e4e9f0c706ac93737fdc0f64642b9ef1/raw/a8c03cf3ea0909a52e431c668d797482d1fd774b/runEmpire.R
+wget https://gist.githubusercontent.com/mjoppich/e4e9f0c706ac93737fdc0f64642b9ef1/raw/a163610e0a7f1b3d70bdc594921b5a3a25294a2a/runEmpire.R
+
+LDFLAGS="-L/usr/local/opt/openblas/lib" CPPFLAGS="-I/usr/local/opt/openblas/include" Rscript runEmpire.R
 
+RSCRIPTPATH=`which Rscript`
 
 if [ $# -gt 2 ]; then
 
@@ -142,7 +152,7 @@ $NCCMD <<EOF
 
   <const id="bindir">${APPBINARYDIR}/</const>
 
-  <execute program="run_msempire" location="" exec="Rscript" param="\${bindir}/runEmpire.R \${msempire_expression_rel} \${msempire_pdata_rel} \${msempire_output_rel} \${msempire_sample_regex}" wsl="WSLsel">
+  <execute program="run_msempire" location="" exec="$RSCRIPTPATH" param="\${bindir}/runEmpire.R \${msempire_expression_rel} \${msempire_pdata_rel} \${msempire_output_rel} \${msempire_sample_regex}" wsl="WSLsel">
     <output type="COUT" color="green" to="outputstream1" />
     <output type="CERR" color="red" to="outputstream2" />
   </execute>

diff --git a/install_templates/install_pureseqtm.igui b/install_templates/install_pureseqtm.igui
@@ -20,7 +20,7 @@ if [ ! "$2" = "" ]; then
 
         echo $2 | sudo -S dpkg --add-architecture i386
         echo $2 | sudo -S apt-get update
-        echo $2 | sudo -S apt-get install libc6:i386 libncurses5:i386 libstdc++6:i386 gcc-multilib
+        echo $2 | sudo -S apt-get -y install libc6:i386 libncurses5:i386 libstdc++6:i386 gcc-multilib
 
     fi
 
@@ -166,7 +166,7 @@ $NCCMD <<EOF
     <if comp="IS_SET" value1="pureseqtm_plot" sep=" "><const>-P 1</const></if>
   </add>
 
-  <execute program="run_pureseqtm" location="" exec="sh" param="\${bindir}/PureseqTM.sh \${cl} wsl="WSLsel">
+  <execute program="run_pureseqtm" location="" exec="sh" param="\${bindir}/PureseqTM.sh" \${cl} wsl="WSLsel">
     <output type="FILE_STD" color="green" location="\${pureseqtm_output}" />
     <output type="CERR" color="red" to="outputstream2" />
   </execute>