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00_binary_compile.sh
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#!/bin/bash
if [ true ]; then
print_red(){
RED='\033[0;31m'
NC='\033[0m' # No Color
printf "${RED}$1${NC}\n"
}
print_green(){
GREEN='\033[0;32m'
NC='\033[0m' # No Color
printf "${GREEN}$1${NC}\n"
}
print_green_no_br(){
GREEN='\033[0;32m'
NC='\033[0m' # No Color
printf "${GREEN}$1${NC}"
}
print_orange(){
ORANGE='\033[0;33m'
NC='\033[0m' # No Color
printf "${ORANGE}$1${NC}\n"
}
print_orange_no_br(){
ORANGE='\033[0;33m'
NC='\033[0m' # No Color
printf "${ORANGE}$1${NC}"
}
print_fluorescent_yellow(){
FLUORESCENT_YELLOW='\033[1;33m'
NC='\033[0m' # No Color
printf "${FLUORESCENT_YELLOW}$1${NC}\n"
}
print_fluorescent_yellow_no_br(){
FLUORESCENT_YELLOW='\033[1;33m'
NC='\033[0m' # No Color
printf "${FLUORESCENT_YELLOW}$1${NC}"
}
print_white(){
WHITE='\033[1;37m'
NC='\033[0m' # No Color
printf "${WHITE}$1${NC}"
}
print_middle(){
FLUORESCENT_YELLOW='\033[1;33m'
NC='\033[0m' # No Color
# 获取终端的宽度
COLUMNS=$(tput cols)
# 遍历每一行
while IFS= read -r line; do
# 计算需要的空格数来居中文本
padding=$(( (COLUMNS - ${#line}) / 2 ))
printf "%${padding}s" ''
printf "${FLUORESCENT_YELLOW}${line}${NC}\n"
done <<< "$1"
}
fi
echo -e "\n\n"
print_middle "The purpose of this script is to \n"
print_middle " 1. assign execute permissions to all users for bash and perl files "
print_middle " 2. compile binaries needed by Shiny app "
print_middle " 3. install python package "
print_middle " 4. check needed tools \n"
print_middle " \n"
if [ -d .git ]; then
git config core.fileMode false
fi
############################ 1. linux dependences #############################
if [ true ]; then
print_green "\n1.Adding some necessary dependencies, please wait a moment..."
print_orange_no_br " Do you want to install Ubuntu dependencies? [y/N]: "
read dependency
dependency=${dependency:-N} # Default to 'N' if no input provided
if [ "$dependency" == "Y" ] || [ "$dependency" == "y" ]; then
print_orange "Installing dependencies..."
# Check for MacOS
if [[ "$OSTYPE" == "darwin"* ]]; then
echo "This is MacOS. No support!"
# Check for Linux
elif [[ "$OSTYPE" == "linux-gnu"* ]]; then
# Source the os-release to get OS information
if [ -f /etc/os-release ]; then
# Load the os-release file
. /etc/os-release
if [[ "$ID" == "ubuntu" || "$ID_LIKE" == "debian" ]]; then
echo "This is a Debian/Ubuntu based distribution. Version: $PRETTY_NAME"
sudo apt update && sudo apt upgrade -y > /dev/null
sudo apt -y install openjdk-21-jdk > /dev/null 2>&1 || print_red " Failed to install openjdk-21-jdk"
# export JAVA_HOME=$(dirname $(dirname $(readlink -f $(which java))))
# export PATH=$PATH:$JAVA_HOME/bin
# 询问用户是否处于调试模式
sudo add-apt-repository -y ppa:alex-p/tesseract-ocr-devel > /dev/null 2>&1 || print_red " Failed to add ppa:alex-p/tesseract-ocr-devel"
sudo apt -y install dpkg > /dev/null 2>&1 || print_red " Failed to install dpkg"
sudo apt -y install zip > /dev/null 2>&1 || print_red " Failed to install zip"
sudo apt -y install build-essential > /dev/null 2>&1 || print_red " Failed to install build-essential"
sudo apt -y install zlib1g-dev > /dev/null 2>&1 || print_red " Failed to install zlib1g-dev"
sudo apt -y install libgdbm-dev > /dev/null 2>&1 || print_red " Failed to install libgdbm-dev"
sudo apt -y install autotools-dev > /dev/null 2>&1 || print_red " Failed to install autotools-dev"
sudo apt -y install automake > /dev/null 2>&1 || print_red " Failed to install automake"
sudo apt -y install nodejs > /dev/null 2>&1 || print_red " Failed to install nodejs"
sudo apt -y install npm > /dev/null 2>&1 || print_red " Failed to install npm"
sudo apt -y install libxml2-dev > /dev/null 2>&1 || print_red " Failed to install libxml2-dev"
sudo apt -y install libxml2 > /dev/null 2>&1 || print_red " Failed to install libxml2"
sudo apt -y install libxslt-dev > /dev/null 2>&1 || print_red " Failed to install libxslt-dev"
sudo apt -y install cmake > /dev/null 2>&1 || print_red " Failed to install cmake"
sudo apt -y install libjpeg-dev > /dev/null 2>&1 || print_red " Failed to install libjpeg-dev "
sudo apt -y install librsvg2-dev > /dev/null 2>&1 || print_red " Failed to install librsvg2-dev"
sudo apt -y install libpoppler-cpp-dev > /dev/null 2>&1 || print_red " Failed to install libpoppler-cpp-dev"
sudo apt -y install freetype2-demos > /dev/null 2>&1 || print_red " Failed to install freetype2-demos"
sudo apt -y install cargo > /dev/null 2>&1 || print_red " Failed to install cargo"
sudo apt -y install libharfbuzz-dev > /dev/null 2>&1 || print_red " Failed to install libharfbuzz-dev"
sudo apt -y install libfribidi-dev > /dev/null 2>&1 || print_red " Failed to install libfribidi-dev"
sudo apt -y install libtesseract-dev > /dev/null 2>&1 || print_red " Failed to install libtesseract-dev"
sudo apt -y install libleptonica-dev > /dev/null 2>&1 || print_red " Failed to install libleptonica-dev"
sudo apt -y install tesseract-ocr-eng > /dev/null 2>&1 || print_red " Failed to install libfribidi-dev"
sudo apt -y install libmagick++-dev > /dev/null 2>&1 || print_red " Failed to install libmagick++-dev"
sudo apt -y install libavfilter-dev > /dev/null 2>&1 || print_red " Failed to install libavfilter-dev"
sudo apt -y install libncurses5-dev > /dev/null 2>&1 || print_red " Failed to install libncurses5-dev"
sudo apt -y install libncursesw5-dev > /dev/null 2>&1 || print_red " Failed to install libncursesw5-dev"
sudo apt -y install libbz2-dev > /dev/null 2>&1 || print_red " Failed to install libbz2-dev"
sudo apt -y install libpcre2-dev > /dev/null 2>&1 || print_red " Failed to install libpcre2-dev"
sudo apt -y install libreadline-dev > /dev/null 2>&1 || print_red " Failed to install libreadline-dev"
sudo apt -y install libssl-dev > /dev/null 2>&1 || print_red " Failed to install libssl-dev"
sudo apt -y install glibc-source > /dev/null 2>&1 || print_red " Failed to install glibc-source"
sudo apt -y install libssl-dev > /dev/null 2>&1 || print_red " Failed to install libssl-dev"
sudo apt -y install libstdc++6 > /dev/null 2>&1 || print_red " Failed to install libstdc++6"
echo "deb http://security.ubuntu.com/ubuntu focal-security main" | sudo tee /etc/apt/sources.list.d/focal-security.list
sudo apt update
sudo apt -y install libssl1.1 > /dev/null 2>&1 || print_red " Failed to install libssl1.1"
sudo apt -y install libcurl4-openssl-dev > /dev/null 2>&1 || print_red " Failed to install libcurl4-openssl-dev"
sudo apt -y install libopenblas-dev > /dev/null 2>&1 || print_red " Failed to install libopenblas-dev"
sudo apt -y install gfortran > /dev/null 2>&1 || print_red " Failed to install gfortran"
sudo update-alternatives --config libblas.so.3-$(arch)-linux-gnu
sudo apt -y install ufw > /dev/null 2>&1 || print_red " Failed to install ufw"
elif [[ "$ID" == "fedora" || "$ID_LIKE" == "fedora" || "$ID" == "rhel" || "$ID_LIKE" == "rhel" ]]; then
echo "This is a Red Hat based distribution. Version: $PRETTY_NAME"
else
echo "This is a Linux distribution but not specifically Debian/Ubuntu or Red Hat based. Version: $PRETTY_NAME"
fi # if [[ "$ID" == "ubuntu" || "$ID_LIKE" == "debian" ]]; then
else # if [ -f /etc/os-release ]; then
echo "Linux distribution, but /etc/os-release not found."
fi # if [ -f /etc/os-release ]; then
# Check for Windows (Cygwin or MinGW)
elif [[ "$OSTYPE" == "cygwin" ]]; then
echo "This is Windows with Cygwin. No support!"
elif [[ "$OSTYPE" == "msys" ]]; then
echo "This is Windows with MinGW. No support!"
# Other unknown OS
else
echo "Unknown Operating System. No support!"
fi
else # if [ "$dependency" == "Y" ] || [ "$dependency" == "y" ]; then
print_fluorescent_yellow " No Linux dependencies installed"
fi
fi
############################ 2. assign execute permissions #############################
print_green_no_br "\n2. Would you like to assign execute permissions to all users for bash and perl files? [Y/n]: "
read -p "" answer
answer=${answer:-Y} # Default to 'Y' if no input provided
if [ "$answer" == "Y" ] || [ "$answer" == "y" ]; then
# 遍历 scripts 目录及其所有子目录中的 .sh 和 .pl 文件
find . -type f \( -name "*.sh" -o -name "*.pl" \) -exec chmod a+x {} \;
else
print_orange "No assignment"
fi
################################## 3. install R #################################
# 检查 R 是否已安装
if [ true ]; then
if ! command -v R >/dev/null 2>&1; then
print_green " \n3. R is not installed. Installing R..."
print_green_no_br "\n1. Would you like to install R (/opt/R/R-4.3.2/bin/R) as Root? [y/N]: "
read -p "" answer
answer=${answer:-N} # Default to 'Y' if no input provided
if [ "$answer" == "Y" ] || [ "$answer" == "y" ]; then
tool_dir=R-4.3.2
tool_link=https://cran.rstudio.com/src/base/R-4/R-4.3.2.tar.gz
wget $tool_link > /dev/null 2>&1 || echo " Failed to download R tar file"
tar -xzvf R-4.3.2.tar.gz > /dev/null 2>&1 || echo " Failed to unzip tar file"
rm R-4.3.2.tar.gz
cd $tool_dir
./configure \
--prefix=/opt/R/$tool_dir \
--enable-R-shlib=yes \
--enable-memory-profiling \
--with-blas \
--with-lapack \
--with-readline=yes \
--with-x=no > /dev/null 2>&1 || echo " Failed to install configure"
make > /dev/null 2>&1 || echo " Failed to make"
sudo make install > /dev/null 2>&1 || echo " Failed to make install"
sudo ln -s /opt/R/$tool_dir/bin/R /usr/local/bin/R
sudo ln -s /opt/R/$tool_dir/bin/Rscript /usr/local/bin/Rscript
cd ..
rm -rf $tool_dir
else
print_orange " Please install R later."
fi #if [ "$answer" == "Y" ] || [ "$answer" == "y" ]; then
else
print_green "\n2. R is already installed."
fi
fi
################################## 4. install python #################################
# 检查 pyhon 是否已安装
if [ true ]; then
# 检测并安装 python3
if ! dpkg -l | grep -q "^ii\s*python3\s"; then
print_green_no_br "\n4. Would you like to install python as Root? [y/N]: "
read -p "" answer
answer=${answer:-N} # Default to 'Y' if no input provided
if [ "$answer" == "Y" ] || [ "$answer" == "y" ]; then
print_green " Installing python3..."
sudo apt -y install python3 > /dev/null 2>&1 || print_red " Failed to install python3"
sudo apt -y install python3-pip > /dev/null 2>&1 || print_red " Failed to install python3-pip"
else
print_orange " Please install python later!"
fi
else
print_green "\n3. python3 is already installed."
fi
fi
################################## 5. compile binary #################################
print_green_no_br "\n5. Would you like to compile PMET and PMETindex binaries? [y/N]:"
if [ true ]; then
read -p " " answer
answer=${answer:-N} # Default to 'N' if no input provided
if [[ "$answer" =~ ^[Yy]$ ]]; then
if [ -f "scripts/pmetindex" ]; then
chmod a+x scripts/pmetindex
chmod a+x scripts/pmet
chmod a+x scripts/fimo
while true; do
print_orange " PMET and PMETindex exist."
print_orange_no_br " Do you want to recompile PMET and PMETindex? [y/N]: "
read -p " " recompile
recompile=${recompile:-N} # Default to 'N' if no input provided
# 检查用户输入是否为 Y, y, N, 或 n
if [[ "$recompile" =~ ^[YyNn]$ ]]; then
break # 如果输入有效，跳出循环
else
print_red " Invalid input. Please enter Y/y for yes or N/n for no."
fi
done
else
print_red " PMETindex and PMET not found. Compile will start..."
recompile=y
fi
if [[ "$recompile" =~ ^[Yy]$ ]]; then
print_orange_no_br " Do you still want to combile PMET and PMETindex? [y/N]: "
read -p "" compile_still
fi
compile_still=${compile_still:-N}
if [[ "$recompile" =~ ^[Yy]$ && "$compile_still" =~ ^[Yy]$ ]]; then
print_fluorescent_yellow "Compiling... It takes minutes."
rm -f scripts/pmetindex
rm -f scripts/pmetParallel
rm -f scripts/pmet
rm -f scripts/fimo
############################# 2.1 fimo with pmet index
print_orange "2.1 Compiling FIMO with PMET homotopic (index) integtated..."
cd src/meme-5.5.3
make distclean > /dev/null 2>&1 #|| print_red " Failed to make distclean"
aclocal > /dev/null 2>&1 || print_red " Failed to aclocal "
automake > /dev/null 2>&1 || print_red " Failed to automake"
currentDir=$(pwd)
if [ -d "$currentDir/build" ]; then
rm -rf "$currentDir/build"
fi
mkdir -p $currentDir/build
chmod a+x ./configure
./configure --prefix=$currentDir/build --enable-build-libxml2 --enable-build-libxslt > /dev/null 2>&1 || print_red " Failed to configure"
make > /dev/null 2>&1 || print_red " Failed to make"
make install > /dev/null 2>&1 || print_red " Failed to make install"
cp build/bin/fimo ../../scripts/
make distclean > /dev/null 2>&1 || print_red " Failed to make distclean"
rm -rf build
# print_orange "make distclean finished...\n"
################################### 2.2 pmetindex
print_orange "2.2 Compiling PMET homotypic (index) binary..."
cd ../indexing
bash build.sh > /dev/null 2>&1
mv bin/pmetindex ../../scripts/
rm -rf bin/*
################################## 2.3 pmetParallel
print_orange "2.3 Compiling PMET heterotypic parallel (pair) binary..."
cd ../pmetParallel
bash build.sh > /dev/null 2>&1
mv bin/pmetParallel ../../scripts/
rm -rf bin/*
# pmet
print_orange "2.4 Compiling PMET heterotypic (pair) binary..."
cd ../pmet
bash build.sh > /dev/null 2>&1
mv bin/pmet ../../scripts/
rm -rf bin/*
# back to home directory
cd ../..
################### 2.4 Check if the compilation was successful
exists=""
not_exists=""
for file in scripts/pmetindex scripts/pmetParallel scripts/pmet scripts/fimo; do
if [ -f "$file" ]; then
exists="$exists\n $file"
else
not_exists="$not_exists\n $file"
fi
done
if [ ! -z "$exists" ]; then
echo -e "\n"
print_green "Compilation Success:$exists"
fi
if [ ! -z "$not_exists" ]; then
echo -e "\n"
print_red "Compilation Failure:$not_exists"
fi
############# 2.5 Give execute permission to all users for the file
chmod a+x scripts/pmetindex
chmod a+x scripts/pmetParallel
chmod a+x scripts/pmet
chmod a+x scripts/fimo
fi # if [[ "$recompile" =~ ^[Yy]$ && "$compile_still" =~ ^[Yy]$ ]]; then
else
print_orange " No tools compiled"
fi # if [[ "$answer" =~ ^[Yy]$ ]]; then
fi
############################# 6. install python packages ##############################
if [ true ]; then
print_green_no_br "\n6. Would you like to install python packages? [y/N]: "
read -p " " answer
answer=${answer:-N} # Default to 'N' if no input provided
if [ "$answer" == "Y" ] || [ "$answer" == "y" ]; then
print_orange "Installing python packages... It takes minutes."
pip install numpy > /dev/null 2>&1 || echo "Failed to install numpy"
pip install pandas > /dev/null 2>&1 || echo "Failed to install pandas"
pip install scipy > /dev/null 2>&1 || echo "Failed to install scipy"
pip install bio > /dev/null 2>&1 || echo "Failed to install bio"
pip install biopython > /dev/null 2>&1 || echo "Failed to install biopython"
else
print_orange " No python packages installed"
fi
fi
################################ 7. check needed tools #################################
if [ true ]; then
print_green "\n7. Checking the execution of GNU Parallel, bedtools, samtools and MEME Suite"
tools=("parallel --version" "bedtools --version" "samtools --version" "fimo -h") # List of tools and their version check commands
missing_tools=() # Initialize an empty array to store tools that cannot be executed
all_tools_found=true
# Iterate over each tool and check if it can be executed
for tool in "${tools[@]}"; do
# Use 'command -v' to check if the tool command is available in the PATH
if ! command -v $tool &> /dev/null; then
echo " $tool could not be found"
all_tools_found=false
missing_tools+=($tool) # Add the tool to the missing tools array
fi
done
# If all tools were found, print a positive message
if $all_tools_found; then
print_orange " All tools were found!"
else
print_fluorescent_yellow_no_br "Would you like to install missing tools? [Y/n]: "
read -p " " answer
answer=${answer:-Y} # Default to 'N' if no input provided
if [ "$answer" == "Y" ] || [ "$answer" == "y" ]; then
# Install the missing tools
for tool in "${missing_tools[@]}"; do
if [ "$tool" == "parallel" ]; then
if [[ "$(uname)" == "Darwin" ]]; then
brew install parallel > /dev/null 2>&1 || print_red " Failed to install bedtools"
elif [[ -f /etc/os-release ]]; then
. /etc/os-release
case $ID in
centos|fedora|rhel)
yum install parallel > /dev/null 2>&1 || print_red " Failed to install bedtools"
;;
debian|ubuntu)
sudo apt update > /dev/null 2>&1 || print_red " Failed to apt update"
sudo apt -y install parallel > /dev/null 2>&1 || print_red " Failed to install bedtools"
;;
*)
echo "Unsupported Linux distribution"
;;
esac
parallel --citation > /dev/null 2>&1 || print_red " Failed to run parallel --citation"
else
echo "Unsupported OS"
fi
fi
if [ "$tool" == "bedtools" ]; then
if [[ "$(uname)" == "Darwin" ]]; then
brew install bedtools > /dev/null 2>&1 || print_red " Failed to install bedtools"
elif [[ -f /etc/os-release ]]; then
. /etc/os-release
case $ID in
centos|fedora|rhel)
yum install BEDTools > /dev/null 2>&1 || print_red " Failed to install bedtools"
;;
debian|ubuntu)
sudo apt update > /dev/null 2>&1 || print_red " Failed to apt update"
sudo apt -y install bedtools > /dev/null 2>&1 || print_red " Failed to install bedtools"
;;
*)
echo "Unsupported Linux distribution"
;;
esac
else
echo "Unsupported OS"
fi
fi
if [ "$tool" == "samtools" ]; then
print_green_no_br "\n1. Would you like to install samtools (~/tools/samtools-1.17/)? [y/N]: "
read -p "" answer
answer=${answer:-Y} # Default to 'Y' if no input provided
if [ "$answer" == "Y" ] || [ "$answer" == "y" ]; then
# 创建 ~/tools 目录，如果运行脚本的用户不是 shiny，则需要修改路径
mkdir -p ~/tools
tool_dir=samtools-1.17
tool_link=https://github.com/samtools/samtools/releases/download/1.17/samtools-1.17.tar.bz2
# 下载并解压 samtools
wget $tool_link -O $tool_dir.tar.bz2 > /dev/null 2>&1 || echo " Failed to download samtools tar file"
tar -xjf $tool_dir.tar.bz2 > /dev/null 2>&1 || echo " Failed to unzip tar file"
rm $tool_dir.tar.bz2
# 进入 samtools 目录并编译
cd $tool_dir && mkdir -p build
./configure --prefix=$(pwd)/build > /dev/null 2>&1 || echo " Failed to configure"
make > /dev/null 2>&1 || echo " Failed to make"
sudo make install > /dev/null 2>&1 || echo " Failed to make install"
# 返回到原始目录并将 samtools 目录移动到 ~/tools 下
cd ..
mv $tool_dir ~/tools/
# 更新 ~/.bashrc 和 ~/.zshrc，添加 samtools 到 PATH
echo "export PATH=~/tools/$tool_dir/build/bin:\$PATH" >> ~/.bashrc
echo "export PATH=~/tools/$tool_dir/build/bin:\$PATH" >> ~/.zshrc
echo "export PATH=~/tools/$tool_dir/build/bin:\$PATH" >> ~/.bash_profile
sudo chown -R shiny:shiny-apps ~/tools/$tool_dir/build/
print_green " samtools successfully installed"
else
print_red " Please install samtools later!"
fi # if [ "$answer" == "Y" ] || [ "$answer" == "y" ]; then
fi # if [ "$tool" == "samtools" ]; then
if [ "$tool" == "fimo" ]; then
print_green_no_br "\n1. Would you like to install MEME suite (~/tools/meme-5.5.2/)? [y/N]: "
read -p "" answer
answer=${answer:-Y} # Default to 'Y' if no input provided
if [ "$answer" == "Y" ] || [ "$answer" == "y" ]; then
mkdir -p ~/tools
tool_dir=meme-5.5.2
tool_link=https://meme-suite.org/meme/meme-software/5.5.2/meme-5.5.2.tar.gz
wget $tool_link > /dev/null 2>&1 || print_red " Failed to download fimo tar file"
tar zxf meme-5.5.2.tar.gz > /dev/null 2>&1 || print_red " Failed to unzip tar file"
rm meme-5.5.2.tar.gz
# 进入 samtools 目录并编译
cd $tool_dir && mkdir -p build
./configure \
--prefix=$(pwd)/build \
--enable-build-libxml2 \
--enable-build-libxslt > /dev/null 2>&1 || echo " Failed to install configure"
make > /dev/null 2>&1 || print_red " Failed to make"
make install > /dev/null 2>&1 || print_red " Failed to make install"
cd ..
mv $tool_dir ~/tools/
echo "export PATH=~/tools/$tool_dir/build/bin:\$PATH" >> ~/.bashrc
echo "export PATH=~/tools/$tool_dir/build/bin:\$PATH" >> ~/.zshrc
echo "export PATH=~/tools/$tool_dir/build/bin:\$PATH" >> ~/.bash_profile
echo "export PATH=~/tools/$tool_dir/build/libexec/meme-5.5.2:\$PATH" >> ~/.bashrc
echo "export PATH=~/tools/$tool_dir/build/libexec/meme-5.5.2:\$PATH" >> ~/.zshrc
echo "export PATH=~/tools/$tool_dir/build/libexec/meme-5.5.2:\$PATH" >> ~/.bash_profile
sudo chown -R shiny:shiny-apps ~/tools/$tool_dir/build/
print_green " MEME Suite successfully installed"
else
print_red " Please install MEME suite later!"
fi # if [ "$answer" == "Y" ] || [ "$answer" == "y" ]; then
fi # # if [ "$tool" == "fimo" ]; then
done
fi
fi
fi
################################## 8. install R packages #################################
if [ true ]; then
# 检查 R 是否已安装
if command -v R >/dev/null 2>&1; then
print_green_no_br "8. Would you like to install R packages? [y/N]: "
# read -p "Would you like to install R packages? [y/N]: " answer
read -p "" answer
answer=${answer:-N} # Default to 'N' if no input provided
if [ "$answer" == "Y" ] || [ "$answer" == "y" ]; then
# 使用 R 脚本检查 rJava 是否已安装
if ! Rscript -e "if (!requireNamespace('rJava', quietly = TRUE)) {quit(status = 1)}"; then
# echo "rJava is not installed. Installing..."
# 重新配置 Java 环境
sudo R CMD javareconf > /dev/null 2>&1
curl -LO https://rforge.net/rJava/snapshot/rJava_1.0-6.tar.gz > /dev/null 2>&1
tar fxz rJava_1.0-6.tar.gz > /dev/null 2>&1
R CMD INSTALL rJava > /dev/null 2>&1 || print_red " Failed to install rJava"
rm rJava_1.0-6.tar.gz
rm -rf rJava
fi
print_orange "Installing R packages... It takes minutes..."
chmod a+x scripts/R_utils/install_packages.R
# Rscript R/utils/install_packages.R
Rscript scripts/R_utils/install_packages.R 2>&1 | tee log_R_packages_installation.log | grep -E "\* DONE \("
awk '/The installed packages are as follows:/{flag=1} flag' log_R_packages_installation.log
else
print_orange " No R packages installed"
fi
else
print_red "\n7. No R packages installed because there is no R installed."
print_fluorescent_yellow " Run 'scripts/R_utils/install_packages.R' to install R packages later. "
fi # if command -v R >/dev/null 2>&1; then
fi
print_green "\nDONE"