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install_dependencies.sh
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#!/bin/bash
# last update: 2024/04/09
set -e -o pipefail
#########################
NANOTRANS_HOME=$(pwd)
BUILD="build"
gpu_support="yes"
mainland_china_installation="no";
#########################
timestamp () {
date +"%F %T"
}
clean () {
dir=$1
if [ -d $dir ]
then
echo "remove previously failed installation in $BUILD/$dir"
rm -rf $dir
fi
}
download () {
url=$1
download_location=$2
echo "Downloading $url to $download_location"
if [[ -f $1 ]];then
# if the tool has been downloaded and deposited in the local, then copy that to destination and install it
echo -n "The tool exists in the local: $1"
cp $1 $2
else
wget -c --no-check-certificate --max-redirect=30 $url -O $download_location
fi
}
clone () {
url=$1
dir=$(basename $url)
echo "run clone for \"git clone $url\""
git clone $url --depth 1
cd $dir
git fetch --unshallow
}
tidy_version () {
echo "$1" | awk -F. '{ printf("%d%03d%03d%03d\n", $1,$2,$3,$4); }';
}
check_installed () {
if [ -e "$1/installed" ]; then
echo "installed"
else
echo ""
fi
}
note_installed () {
touch "$1/installed"
}
install_r_pkg () {
if [ -z $(check_installed "$rlib_dir/$1") ]; then
echo "[$(timestamp)] Installing $1 (R package)..."
clean "$rlib_dir/$1"
R -e "install.packages(\"$1\", repos=\"http://cran.rstudio.com/\", lib=\"$build_dir/R_libs/\")"
note_installed "$rlib_dir/$1"
fi
}
install_r_pkg_source () {
if [ -z $(check_installed "$rlib_dir/$1") ]; then
echo "[$(timestamp)] Installing $1 (R package)..."
clean "$rlib_dir/$1"
url_source_rpkg="https://cran.r-project.org/src/contrib/Archive/$1/${1}_${2}.tar.gz"
R -e "install.packages(\"$url_source_rpkg\", repos=NULL, type=\"source\", lib=\"$build_dir/R_libs/\")"
note_installed "$rlib_dir/$1"
fi
}
#install_r_pke_byBiocManager () {
# if [ -z $(check_installed "$rlib_dir/$1") ]; then
# echo "[$(timestamp)] Installing $1 (R package)..."
# clean "$rlib_dir/$1"
# R -e ".libPaths(\"$build_dir/R_libs/\"); BiocManager::install(\"$1\", lib=\"$build_dir/R_libs/\")"
# note_installed "$rlib_dir/$1"
# fi
#}
# aim: marking that pkg (python) has beed installed successfully through conda
install_pkg_byconda () {
if [ ! -d $site_packages/$1 ]; then mkdir -p $site_packages/$1 ; fi
if [ -z $(check_installed $site_packages/$1) ]; then
echo "[$(timestamp)] Installing $1 ..."
source $miniconda3_dir/activate $build_dir/miniconda3
$miniconda3_dir/conda install -y -c conda-forge -c bioconda $1=$2
source $miniconda3_dir/deactivate
fi
note_installed $site_packages/$1
}
install_and_create_pkg_condaenv () {
if [ -z $(check_installed $build_dir/${1}_conda_env/bin) ]; then
echo "[$(timestamp)] Installing $1 ..."
cd $build_dir
$miniconda3_dir/conda create -y -p $build_dir/${1}_conda_env
source $miniconda3_dir/activate $build_dir/${1}_conda_env
$miniconda3_dir/conda install -y -c conda-forge -c bioconda $1=$2
source $miniconda3_dir/deactivate
note_installed $build_dir/${1}_conda_env/bin
fi
}
echo ""
echo ""
echo "##################################################################"
echo "### ###"
echo "### Welcome to NanoTrans ###"
echo "### ###"
echo "##################################################################"
echo ""
echo ""
echo ""
echo ""
echo "[$(timestamp)] Performing gcc version check .."
GCC_VERSION=$(gcc -dumpversion)
if [[ $(tidy_version "$GCC_VERSION") -ge $(tidy_version "4.9.0") ]]
then
echo "Detected gcc version: $GCC_VERSION."
echo "NanoTrans requires gcc version >= 4.9."
echo "Requirement satisfied."
echo "Installation continues .."
else
echo "Detected gcc version: $GCC_VERSION."
echo "NanoTrans requires gcc version >= 4.9."
echo "Requirement unsatisfied"
echo "Please upgrade your gcc version. Installation Terminates!"
echo "Exit!"
exit 1
fi
echo ""
echo ""
echo "[$(timestamp)] Installation starts ..."
echo ""
while getopts ":hgca" opt
do
case "${opt}" in
h)
echo "Usage:"
echo "bash install_dependencies.sh"
echo "When running installation with CUDA GPU support, please run this script with the '-g' option >"
echo "bash install_dependencies.sh -g"
echo "When running installation without CUDA GPU support, please run this script with the '-c' option >"
echo "bash install_dependencies.sh -c"
echo "When running installation within mainland China and use alternative conda repository sources, please run this script with the '-a' option >"
echo "bash install_dependencies.sh -a";;
g)
echo "Detected the '-g' option >"
echo "Set gpu_support as 'yes'"
gpu_support="yes";;
c)
echo "Detected the '-c' option >"
echo "Set gpu_support as 'no'"
gpu_support="no";;
a)
echo "Detected the '-a' option >"
echo "Set installation location as 'mainland_china' and use alternative conda repository sources"
mainland_china_installation="yes";;
esac
done
echo "";
# echo "mainland_china_installation=$mainland_china_installation"
if [ -z "$MAKE_JOBS" ]
then
echo "[$(timestamp)] Defaulting to 2 concurrent jobs when executing make. Override with MAKE_JOBS=<NUM>"
MAKE_JOBS=2
fi
if [ ! -z "$INSTALL_DEPS" ]; then
echo "Installing ONT build dependencies for Debian/Ubuntu."
echo "sudo privileges are required and you will be prompted to enter your password"
sudo apt-get update
xargs -a debiandeps sudo apt-get install -y
fi
MINICONDA3_VERSION="py39_23.11.0-2" # released on 2023.11.16
if [[ "$mainland_china_installation" == "no" ]]
then
MINICONDA3_DOWNLOAD_URL="https://repo.anaconda.com/miniconda/Miniconda3-${MINICONDA3_VERSION}-Linux-x86_64.sh"
else
MINICONDA3_DOWNLOAD_URL="https://mirrors.tuna.tsinghua.edu.cn/anaconda/miniconda/Miniconda3-${MINICONDA3_VERSION}-Linux-x86_64.sh"
fi
# for reads preparation and preprocessing
BLAST_VERSION="2.2.31" #
BLAST_DOWNLOAD_URL="https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${BLAST_VERSION}/ncbi-blast-${BLAST_VERSION}+-x64-linux.tar.gz"
# RMBLAST_VERSION="2.2.28" #
# RMBLAST_DOWNLOAD_URL="http://ftp.ncbi.nlm.nih.gov/blast/executables/rmblast/${RMBLAST_VERSION}/ncbi-rmblastn-${RMBLAST_VERSION}-x64-linux.tar.gz"
# SRA_VERSION="3.0.0" # released on 2022.02.10
# SRA_DOWNLOAD_URL="https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/${SRA_VERSION}/sratoolkit.${SRA_VERSION}-centos_linux64.tar.gz"
TRIMMOMATIC_VERSION="0.38" #
TRIMMOMATIC_DOWNLOAD_URL="http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-${TRIMMOMATIC_VERSION}.zip"
BPIPE_VERSION="0.9.9.2"
BPIPE_DOWNLOAD_URL="https://github.com/ssadedin/bpipe/releases/download/${BPIPE_VERSION}/bpipe-${BPIPE_VERSION}.tar.gz"
VELVET_VERSION="1.2.10"
VELVET_DOWNLOAD_URL="https://github.com/dzerbino/velvet/archive/v${VELVET_VERSION}.tar.gz"
OASES_VERSION="0.2.09"
OASES_DOWNLOAD_URL="https://github.com/dzerbino/oases/archive/refs/tags/${OASES_VERSION}.tar.gz"
BOWTIE2_VERSION="2.4.5"
BOWTIE2_DOWNLOAD_URL="https://github.com/BenLangmead/bowtie2/releases/download/v${BOWTIE2_VERSION}/bowtie2-${BOWTIE2_VERSION}-linux-x86_64.zip"
#FASTXTK_VERSION="0.0.13_binaries_Linux_2.6_amd64"
#FASTXTK_DOWNLOAD_URL="http://hannonlab.cshl.edu/fastx_toolkit/fastx_toolkit_${FASTXTK_VERSION}.tar.bz2"
FASTXTK_VERSION="0.0.14"
BBMAP_VERSION="39.00"
BBMAP_DOWNLOAD_URL="https://sourceforge.net/projects/bbmap/files/BBMap_${BBMAP_VERSION}.tar.gz"
# basecalling
GUPPY_VERSION="6.2.1" # released on 2022.06.07
#if [[ "$gpu_support" == "yes" ]]
#then
GUPPY_GPU_DOWNLOAD_URL="https://mirror.oxfordnanoportal.com/software/analysis/ont-guppy_${GUPPY_VERSION}_linux64.tar.gz"
#else
GUPPY_CPU_DOWNLOAD_URL="https://mirror.oxfordnanoportal.com/software/analysis/ont-guppy-cpu_${GUPPY_VERSION}_linux64.tar.gz"
#fi
DORADO_VERSION="0.6.0" # released on 2024.04.02
DORADO_DOWNLOAD_URL="https://cdn.oxfordnanoportal.com/software/analysis/dorado-${DORADO_VERSION}-linux-x64.tar.gz"
# QC
NANOPLOT_VERSION="1.40.0" # released on 2022.04.08
# NANOFILT_VERSION="2.8.0" # released on 2021.02.26
#NUMPY_VERSION="1.16.3"
SCIPY_VERSION="1.2.1"
NANOPOLISH_VERSION="0.14.0" # released on 2022.05.25
NANOPOLISH_GITHUB_VERSION="07cb03d"
FLAIR_VERSION="2.0.0" #
GFFREAD_VERSION="0.12.7" # released on 2021.07.23
GFFREAD_DOWNLOAD_URL="https://ccb.jhu.edu/software/stringtie/dl/gffread-${GFFREAD_VERSION}.Linux_x86_64.tar.gz"
PICARD_VERSION="2.27.4" # released on 2022.06.30
PICARD_DOWNLOAD_URL="https://github.com/broadinstitute/picard/releases/download/${PICARD_VERSION}/picard.jar"
# SEQTK_DOWNLOAD_URL="https://github.com/lh3/seqtk"
# SEQTK_GITHUB_COMMIT_VERSION="7c04ce7" # commited on 2021.03.23
XPORE_VERSION="2.1"
JAFFAL_VERSION="2.3"
JAFFAL_DOWNLOAD_URL="https://github.com/Oshlack/JAFFA/releases/download/version-${JAFFAL_VERSION}/JAFFA-version-${JAFFAL_VERSION}.tar.gz"
# UCSC Utilities
BEDPARTITION_DOWNLOAD_URL="http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedPartition"
GTFTOGENEPRED_DOWNLOAD_URL="http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/gtfToGenePred"
BLAT_DOWNLOAD_URL="http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/blat"
# pkgs used in generating HTML reports
QUARTO_VERSION="1.3.450"
# Create the $BUILD directory for dependency installation
if [ -d $BUILD ]
then
echo ""
echo "[$(timestamp)] Detected previously generated $BUILD directory."
else
echo "[$(timestamp)] Create the new $BUILD directory."
mkdir $BUILD
echo ""
fi
cd $BUILD
build_dir=$(pwd)
echo ""
echo "[$(timestamp)] Download and install all the dependencies"
echo ""
# Downloading all the dependencies
# ---------- set Perl & Python environment variables -------------
PYTHONPATH="$build_dir"
PERL5LIB="$build_dir:$PERL5LIB"
PERL5LIB="$build_dir/cpanm/perlmods/lib/perl5:$PERL5LIB"
echo ""
echo "[$(timestamp)] Installing Perl modules ..."
cpanm_dir=$build_dir/cpanm
mkdir -p $cpanm_dir
if [ -z $(check_installed $cpanm_dir) ]; then
cd $cpanm_dir
# wget -c --no-check-certificate -O - https://cpanmin.us/ > cpanm
# work around for the unstable downloading issue
cp $NANOTRANS_HOME/misc/cpanm .
########
chmod +x cpanm
mkdir -p perlmods
$cpanm_dir/cpanm -l $cpanm_dir/perlmods --prompt --notest --skip-installed Test::[email protected]
$cpanm_dir/cpanm -l $cpanm_dir/perlmods --prompt --notest --skip-installed [email protected]
$cpanm_dir/cpanm -l $cpanm_dir/perlmods --prompt --skip-installed Statistics::[email protected]
$cpanm_dir/cpanm -l $cpanm_dir/perlmods --prompt --skip-installed Statistics::Descriptive::[email protected]
# $cpanm_dir/cpanm -l $cpanm_dir/perlmods --skip-installed Math::[email protected]
# $cpanm_dir/cpanm -l $cpanm_dir/perlmods --skip-installed Math::[email protected]
note_installed $cpanm_dir
fi
echo ""
echo "[$(timestamp)] Installing R libraries ..."
which R || echo "Please install R first."
r_path=$(which R)
rlib_dir="$build_dir/R_libs"
mkdir -p $rlib_dir
cd $rlib_dir
R_VERSION=$(R --version |head -1 |cut -d " " -f 3)
if [ $(tidy_version "$R_VERSION") -ge $(tidy_version "3.6.0") ]; then
if [ -z $(check_installed "$rlib_dir/BiocManager") ]; then
clean "$rlib_dir/BiocManager"
echo "R_VERSION=$R_VERSION, use the new bioconductor installation protocol"
R -e ".libPaths(\"$build_dir/R_libs/\");install.packages(\"BiocManager\", repos=\"http://cran.rstudio.com/\", lib=\"$build_dir/R_libs/\")";
note_installed "$rlib_dir/BiocManager"
fi
else
die "R >= v3.6.0 is needed! Exit!"
fi
#if [ -z $(check_installed "$rlib_dir/optparse") ]; then
# clean "$rlib_dir/optparse"
# R -e "install.packages(\"optparse\", repos=\"http://cran.rstudio.com/\", lib=\"$build_dir/R_libs/\")"
# note_installed "$rlib_dir/optparse"
#fi
# if [ -z $(check_installed "$rlib_dir/RColorBrewer") ]; then
# clean "$rlib_dir/RColorBrewer"
# R -e "install.packages(\"RColorBrewer\", repos=\"http://cran.rstudio.com/\", lib=\"$build_dir/R_libs/\")"
# note_installed "$rlib_dir/RColorBrewer"
# fi
#if [ -z $(check_installed "$rlib_dir/ggplot2") ]; then
# clean "$rlib_dir/ggplot2"
# R -e "install.packages(\"ggplot2\", repos=\"http://cran.rstudio.com/\", lib=\"$build_dir/R_libs/\")"
# note_installed "$rlib_dir/ggplot2"
#fi
#
#if [ -z $(check_installed "$rlib_dir/ggrepel") ]; then
# clean "$rlib_dir/ggrepel"
# R -e "install.packages(\"ggrepel\", repos=\"http://cran.rstudio.com/\", lib=\"$build_dir/R_libs/\")"
# note_installed "$rlib_dir/ggrepel"
#fi
#
#if [ -z $(check_installed "$rlib_dir/dplyr") ]; then
# clean "$rlib_dir/dplyr"
# R -e "install.packages(\"dplyr\", repos=\"http://cran.rstudio.com/\", lib=\"$build_dir/R_libs/\")"
# note_installed "$rlib_dir/dplyr"
#fi
# if [ -z $(check_installed "$rlib_dir/samplesizeCMH") ]; then
# clean "$rlib_dir/samplesizeCMH"
# R -e "install.packages(\"samplesizeCMH\", repos=\"http://cran.rstudio.com/\", lib=\"$build_dir/R_libs/\")"
# note_installed "$rlib_dir/samplesizeCMH"
# fi
install_r_pkg optparse
install_r_pkg ggplot2
install_r_pkg ggrepel
install_r_pkg dplyr
install_r_pkg data.table
install_r_pkg_source ggseqlogo "0.1"
install_r_pkg DT
install_r_pkg tidyr
install_r_pkg tibble
install_r_pkg generics
# ------------- Miniconda3 --------------------
echo ""
echo "[$(timestamp)] Installing miniconda3 ..."
miniconda3_dir="$build_dir/miniconda3/bin"
if [ -z $(check_installed $miniconda3_dir) ]; then
cd $build_dir
clean "$build_dir/miniconda3"
download $MINICONDA3_DOWNLOAD_URL "Miniconda3-${MINICONDA3_VERSION}-Linux-x86_64.sh"
bash Miniconda3-${MINICONDA3_VERSION}-Linux-x86_64.sh -b -p $build_dir/miniconda3
if [[ "$mainland_china_installation" == "yes" ]]
then
$miniconda3_dir/conda config --add channels https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
$miniconda3_dir/conda config --add channels https://mirrors.bfsu.edu.cn/anaconda/pkgs/free
$miniconda3_dir/conda config --add channels https://mirrors.bfsu.edu.cn/anaconda/pkgs/pro
$miniconda3_dir/conda config --add channels https://mirrors.bfsu.edu.cn/anaconda/pkgs/msys2
$miniconda3_dir/conda config --add channels https://mirrors.bfsu.edu.cn/anaconda/cloud/bioconda
$miniconda3_dir/conda config --add channels https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
$miniconda3_dir/conda config --add channels https://anaconda.mirrors.sjtug.sjtu.edu.cn/pkgs/main
$miniconda3_dir/conda config --add channels https://anaconda.mirrors.sjtug.sjtu.edu.cn/pkgs/free
$miniconda3_dir/conda config --add channels https://anaconda.mirrors.sjtug.sjtu.edu.cn/pkgs/pro
$miniconda3_dir/conda config --add channels https://anaconda.mirrors.sjtug.sjtu.edu.cn/pkgs/msys2
$miniconda3_dir/conda config --add channels https://anaconda.mirrors.sjtug.sjtu.edu.cn/cloud/bioconda
$miniconda3_dir/conda config --add channels https://anaconda.mirrors.sjtug.sjtu.edu.cn/cloud/conda-forge
else
$miniconda3_dir/conda config --add channels defaults
$miniconda3_dir/conda config --add channels bioconda
$miniconda3_dir/conda config --add channels conda-forge
fi
$miniconda3_dir/conda config --set show_channel_urls yes
$miniconda3_dir/conda config --set ssl_verify no
$miniconda3_dir/conda config --set channel_priority flexible
cd $build_dir
rm Miniconda3-${MINICONDA3_VERSION}-Linux-x86_64.sh
note_installed $miniconda3_dir
fi
# --------------- ncbi-blast+ ------------------
echo ""
echo "[$(timestamp)] Installing ncbi-blast+ ..."
blast_dir="$build_dir/ncbi-blast-${BLAST_VERSION}+/bin"
windowmasker_dir="$build_dir/ncbi-blast-${BLAST_VERSION}+/bin"
if [ -z $(check_installed $blast_dir) ]; then
cd $build_dir
clean "$build_dir/ncbi-blast-${BLAST_VERSION}+"
echo ""
echo "Installing ncbi-blast+ ..."
echo "Download ncbi-blast-v${BLAST_VERSION}"
download $BLAST_DOWNLOAD_URL "ncbi-blast-${BLAST_VERSION}+-x64-linux.tar.gz"
tar xvzf ncbi-blast-${BLAST_VERSION}+-x64-linux.tar.gz
cd $build_dir
rm ncbi-blast-${BLAST_VERSION}+-x64-linux.tar.gz
note_installed $blast_dir
fi
# # --------------- ncbi-rmblast ------------------
# echo ""
# echo "[$(timestamp)] Installing ncbi-rmblast ..."
# rmblast_dir="$build_dir/ncbi-rmblastn-${RMBLAST_VERSION}/bin"
# if [ -z $(check_installed $rmblast_dir) ]; then
# cd $build_dir
# clean "$build_dir/ncbi-rmblastn-${RMBLAST_VERSION}"
# echo ""
# echo "Installing ncbi-rmblastn ..."
# echo "Download ncbi-rmblastn-v${BLAST_VERSION}"
# download $RMBLAST_DOWNLOAD_URL "ncbi-rmblastn-${RMBLAST_VERSION}-x64-linux.tar.gz"
# tar xvzf ncbi-rmblastn-${RMBLAST_VERSION}-x64-linux.tar.gz
# # copy rmblastn binary file to ncbi-blast+ directory for easy RepeatMasker configuration
# cp $rmblast_dir/rmblastn $blast_dir
# cd $build_dir
# rm ncbi-rmblastn-${RMBLAST_VERSION}-x64-linux.tar.gz
# note_installed $rmblast_dir
# fi
# # ------------- SRA Toolkit -------------------
# echo ""
# echo "[$(timestamp)] Installing SRAtoolkit ..."
# sra_dir="$build_dir/sratoolkit.${SRA_VERSION}-centos_linux64/bin"
# if [ -z $(check_installed $sra_dir) ]; then
# cd $build_dir
# echo "Download SRAtoolkit-v${SRA_VERSION}"
# download $SRA_DOWNLOAD_URL sratoolkit.${SRA_VERSION}-centos_linux64.tar.gz
# tar xvzf sratoolkit.${SRA_VERSION}-centos_linux64.tar.gz
# rm sratoolkit.${SRA_VERSION}-centos_linux64.tar.gz
# note_installed $sra_dir
# fi
# --------------- Trimmomatic -----------------
echo ""
echo "[$(timestamp)] Installing Trimmomatic ..."
trimmomatic_dir="$build_dir/Trimmomatic-${TRIMMOMATIC_VERSION}"
if [ -z $(check_installed $trimmomatic_dir) ]; then
cd $build_dir
clean "$build_dir/Trimmomatic-${TRIMMOMATIC_VERSION}"
echo "Download Trimmomatic-v${TRIMMOMATIC_VERSION}"
download $TRIMMOMATIC_DOWNLOAD_URL "Trimmomatic-${TRIMMOMATIC_VERSION}.zip"
unzip Trimmomatic-${TRIMMOMATIC_VERSION}.zip
cd $trimmomatic_dir
chmod 755 trimmomatic-${TRIMMOMATIC_VERSION}.jar
ln -s trimmomatic-${TRIMMOMATIC_VERSION}.jar trimmomatic.jar
echo "java -XX:ParallelGCThreads=4 -jar $trimmomatic_dir/trimmomatic-${TRIMMOMATIC_VERSION}.jar \$*" > trimmomatic
chmod 755 trimmomatic
cd $build_dir
rm Trimmomatic-${TRIMMOMATIC_VERSION}.zip
note_installed $trimmomatic_dir
fi
#--------------- Guppy-GPU --------------------
echo ""
echo "[$(timestamp)] Installing guppy-GPU ..."
guppy_gpu_dir="$build_dir/ont-guppy-gpu/bin"
if [ -z $(check_installed $guppy_gpu_dir) ]; then
cd $build_dir
clean "$build_dir/ont-guppy-gpu"
echo "Download Guppy-v${GUPPY_VERSION}"
download $GUPPY_GPU_DOWNLOAD_URL "ont-guppy_${GUPPY_VERSION}_linux64.tar.gz"
tar xvzf ont-guppy_${GUPPY_VERSION}_linux64.tar.gz
mv ont-guppy ont-guppy-gpu
rm ont-guppy_${GUPPY_VERSION}_linux64.tar.gz
note_installed $guppy_gpu_dir
fi
# --------------- Guppy-CPU --------------------
echo ""
echo "[$(timestamp)] Installing guppy-CPU ..."
guppy_cpu_dir="$build_dir/ont-guppy-cpu/bin"
if [ -z $(check_installed $guppy_cpu_dir) ]; then
cd $build_dir
clean "$build_dir/ont-guppy-cpu"
echo "Download Guppy-v${GUPPY_VERSION}"
download $GUPPY_CPU_DOWNLOAD_URL "ont-guppy_${GUPPY_VERSION}_linux64.tar.gz"
tar xvzf ont-guppy_${GUPPY_VERSION}_linux64.tar.gz
rm ont-guppy_${GUPPY_VERSION}_linux64.tar.gz
note_installed $guppy_cpu_dir
fi
# -------------------- Dorado --------------------
echo ""
echo "[$(timestamp)] Installing Dorado ..."
dorado_dir="$build_dir/dorado-${DORADO_VERSION}-linux-x64/bin"
if [ -z $(check_installed $dorado_dir) ]; then
cd $build_dir
clean "$build_dir/dorado-${DORADO_VERSION}-linux-x64/"
echo "Download Dorado-v${GUPPY_VERSION}"
download $DORADO_DOWNLOAD_URL "dorado-${DORADO_VERSION}-linux-x64.tar.gz"
tar xvzf dorado-${DORADO_VERSION}-linux-x64.tar.gz
rm dorado-${DORADO_VERSION}-linux-x64.tar.gz
note_installed $dorado_dir
fi
# # ------------- seqtk -------------------
# echo ""
# echo "[$(timestamp)] Installing seqtk ..."
# seqtk_dir="$build_dir/seqtk"
# if [ -z $(check_installed $seqtk_dir) ]; then
# cd $build_dir
# clean "$build_dir/seqtk"
# echo "Download SEQTK-v${SEQTK_VERSION}"
# git clone $SEQTK_DOWNLOAD_URL
# cd seqtk
# git checkout -f -q $SEQTK_GITHUB_COMMIT_VERSION
# make
# cd $build_dir
# note_installed $seqtk_dir
# fi
# # --------------- Nanofilt --------------------
# echo ""
# echo "[$(timestamp)] Installing NanoFilt ..."
# nanofilt_dir="$build_dir/nanofilt_conda_env/bin"
# if [ -z $(check_installed $nanofilt_dir) ]; then
# cd $build_dir
# $miniconda3_dir/conda create -y -p $build_dir/nanofilt_conda_env
# source $miniconda3_dir/activate $build_dir/nanofilt_conda_env
# $miniconda3_dir/conda install -y -c bioconda nanofilt=${NANOFILT_VERSION}
# source $miniconda3_dir/deactivate
# note_installed $nanofilt_dir
# fi
# --------------- Nanoplot --------------------
echo ""
echo "[$(timestamp)] Installing NanoPlot ..."
nanoplot_dir="$build_dir/nanoplot_conda_env/bin"
if [ -z $(check_installed $nanoplot_dir) ]; then
cd $build_dir
$miniconda3_dir/conda create -y -p $build_dir/nanoplot_conda_env python=3.9
source $miniconda3_dir/activate $build_dir/nanoplot_conda_env
$miniconda3_dir/conda install -y -c bioconda nanoplot=${NANOPLOT_VERSION}
source $miniconda3_dir/deactivate
note_installed $nanoplot_dir
fi
# --------------- Picard -----------------
echo ""
echo "[$(timestamp)] Installing picard ..."
picard_dir="$build_dir/Picard-v${PICARD_VERSION}"
if [ -z $(check_installed $picard_dir) ]; then
cd $build_dir
clean "$build_dir/Picard-v${PICARD_VERSION}"
echo "Download Picard-v${PICARD_VERSION}"
download $PICARD_DOWNLOAD_URL "picard.jar"
mkdir Picard-v${PICARD_VERSION}
mv picard.jar $picard_dir
cd $picard_dir
chmod 755 picard.jar
note_installed $picard_dir
fi
# --------------- gffread ------------------
echo ""
echo "[$(timestamp)] Installing gffread ..."
gffread_dir="$build_dir/gffread"
if [ -z $(check_installed $gffread_dir) ]; then
cd $build_dir
clean "$build_dir/gffread"
echo "Download gffread-v${GFFREAD_VERSION}"
download $GFFREAD_DOWNLOAD_URL "gffread-${GFFREAD_VERSION}.Linux_x86_64.tar.gz"
tar xzf gffread-${GFFREAD_VERSION}.Linux_x86_64.tar.gz
mv gffread-${GFFREAD_VERSION}.Linux_x86_64 gffread
cd $build_dir
rm gffread-${GFFREAD_VERSION}.Linux_x86_64.tar.gz
note_installed $gffread_dir
fi
# -------------- Nanopolish ----------------
echo ""
echo "[$(timestamp)] Installing Nanopolish ..."
nanopolish_dir="$build_dir/nanopolish_conda_env/bin"
if [ -z $(check_installed $nanopolish_dir) ]; then
cd $build_dir
clean "$build_dir/nanopolish_conda_env"
$miniconda3_dir/conda create -y -p $build_dir/nanopolish_conda_env python=3.9
source $miniconda3_dir/activate $build_dir/nanopolish_conda_env
$miniconda3_dir/conda install -y -c bioconda nanopolish=${NANOPOLISH_VERSION}
source $miniconda3_dir/deactivate
note_installed $nanopolish_dir
fi
# --------------- XPORE -----------------
echo ""
echo "[$(timestamp)] Installing XPORE ..."
xpore_dir="$build_dir/xpore_conda_env/bin"
if [ -z $(check_installed $xpore_dir) ]; then
cd $build_dir
clean "$build_dir/xpore_conda_env"
echo "Download XPORE-v${XPORE_VERSION}"
$miniconda3_dir/conda create -y -p $build_dir/xpore_conda_env python=3.9
source $miniconda3_dir/activate $build_dir/xpore_conda_env
$miniconda3_dir/conda install -y -c bioconda xpore=${XPORE_VERSION}
source $miniconda3_dir/deactivate
note_installed $xpore_dir
fi
# --------------- flair -----------------
echo ""
echo "[$(timestamp)] Installing flair ..."
flair_dir="$build_dir/flair_conda_env/bin"
minimap2_dir="$build_dir/flair_conda_env/bin"
samtools_dir="$build_dir/flair_conda_env/bin"
bedtools_dir="$build_dir/flair_conda_env/bin"
if [ -z $(check_installed $flair_dir) ]; then
cd $build_dir
clean "$build_dir/flair_conda_env"
echo "Download flair-v${FLAIR_VERSION}"
$miniconda3_dir/conda create -y -p $build_dir/flair_conda_env python=3.9
source $miniconda3_dir/activate $build_dir/flair_conda_env
$miniconda3_dir/conda install -y -c conda-forge -c bioconda flair=${FLAIR_VERSION}
source $miniconda3_dir/deactivate
# fix a bug of flair
cd $flair_dir
head -1 bam2Bed12 > bam2Bed12.header
tail -n +2 $NANOTRANS_HOME/misc/bam2Bed12 >bam2Bed12.content
cat bam2Bed12.header bam2Bed12.content > bam2Bed12
chmod a+x bam2Bed12
rm bam2Bed12.header
rm bam2Bed12.content
# turn on pdf output for plot_isoform_usage
cp $NANOTRANS_HOME/misc/plot_isoform_usage_for_pdf plot_isoform_usage
# fix a bug in subset_unassigned_reads.py
cd $build_dir/flair_conda_env/lib/python3.9/site-packages/flair
sed -i -e "25s/$/[:line[3].rfind(';')]/" -e "27s/$/[:line[9].rfind(';')]/" subset_unassigned_reads.py
note_installed $flair_dir
fi
# --------------- rna modification deps -----------------
site_packages="$build_dir/site_packages"
mkdir -p $site_packages
# pkgs used in plotting characteristics of rna modifications
CYUSHUFFLE_VERSION="1.1.2"
PYSAM_VERSION="0.22.0"
TABIX_VERSION="1.11"
MATPLOTLIB_VERSION="3.8.2"
NUMPY_VERSION="1.26.0"
PANDAS_VERSION="2.1.4"
install_pkg_byconda pysam $PYSAM_VERSION
install_pkg_byconda tabix $TABIX_VERSION
install_pkg_byconda matplotlib $MATPLOTLIB_VERSION
install_pkg_byconda numpy $NUMPY_VERSION
install_pkg_byconda pandas $PANDAS_VERSION
install_pkg_byconda cyushuffle $CYUSHUFFLE_VERSION
# --------------- bpipe ------------------
echo ""
echo "[$(timestamp)] Installing bpipe ..."
bpipe_dir="$build_dir/bpipe-${BPIPE_VERSION}/bin"
if [ -z $(check_installed $bpipe_dir) ]; then
cd $build_dir
clean "$build_dir/bpipe-${BPIPE_VERSION}"
echo "Download bpipe-v${BPIPE_VERSION}"
download $BPIPE_DOWNLOAD_URL "bpipe-${BPIPE_VERSION}.tar.gz"
tar xzf bpipe-${BPIPE_VERSION}.tar.gz
rm bpipe-${BPIPE_VERSION}.tar.gz
note_installed $bpipe_dir
fi
# --------------- velvet ------------------
echo ""
echo "[$(timestamp)] Installing velvet ..."
velvet_dir="$build_dir/velvet-${VELVET_VERSION}"
if [ -z $(check_installed $velvet_dir) ]; then
cd $build_dir
clean "$build_dir/velvet-${VELVET_VERSION}"
echo "Download velvet-v${VELVET_VERSION}"
download $VELVET_DOWNLOAD_URL "velvet-${VELVET_VERSION}.tar.gz"
tar xzf velvet-${VELVET_VERSION}.tar.gz
cd "$build_dir/velvet-${VELVET_VERSION}"
make MAXKMERLENGTH=37 LONGSEQUENCES=1 #OPENMP=1
cd $build_dir
rm velvet-${VELVET_VERSION}.tar.gz
note_installed $velvet_dir
fi
# --------------- oases ------------------
echo ""
echo "[$(timestamp)] Installing oases ..."
oases_dir="$build_dir/oases-${OASES_VERSION}"
if [ -z $(check_installed $oases_dir) ]; then
cd $build_dir
clean "$build_dir/oases-${OASES_VERSION}"
echo "Download oases-v${OASES_VERSION}"
download $OASES_DOWNLOAD_URL "oases-${OASES_VERSION}.tar.gz"
tar xzf oases-${OASES_VERSION}.tar.gz
cd "$build_dir/oases-${OASES_VERSION}"
make MAXKMERLENGTH=37 LONGSEQUENCES=1 "VELVET_DIR=$build_dir/velvet-${VELVET_VERSION}" #OPENMP=1
cd $build_dir
rm oases-${OASES_VERSION}.tar.gz
note_installed $oases_dir
fi
# --------------- bowtie2 ------------------
echo ""
echo "[$(timestamp)] Installing bowtie2 ..."
bowtie2_dir="$build_dir/bowtie2-${BOWTIE2_VERSION}-linux-x86_64"
if [ -z $(check_installed $bowtie2_dir) ]; then
cd $build_dir
clean "$build_dir/bowtie2-${BOWTIE2_VERSION}"
echo "Download bowtie2-v${BOWTIE2_VERSION}"
download $BOWTIE2_DOWNLOAD_URL "bowtie2-${BOWTIE2_VERSION}-linux-x86_64.zip"
unzip bowtie2-${BOWTIE2_VERSION}-linux-x86_64.zip
cd $build_dir
rm bowtie2-${BOWTIE2_VERSION}-linux-x86_64.zip
note_installed $bowtie2_dir
fi
# --------------- fastx_toolkit ------------------
echo ""
#echo "[$(timestamp)] Installing fastx_toolkit ..."
#fastxtk_dir="$build_dir/fastx_toolkit/bin"
#if [ -z $(check_installed $fastxtk_dir) ]; then
# cd $build_dir
# clean "$build_dir/fastx_toolkit"
# mkdir fastx_toolkit
# cd fastx_toolkit
# echo "Download fastx_toolkit-v${FASTXTK_VERSION}"
# download $FASTXTK_DOWNLOAD_URL "fastx_toolkit_${FASTXTK_VERSION}.tar.bz2"
# tar -xjf fastx_toolkit_${FASTXTK_VERSION}.tar.bz2
# rm fastx_toolkit_${FASTXTK_VERSION}.tar.bz2
# note_installed $fastxtk_dir
#fi
install_pkg_byconda fastx_toolkit $FASTXTK_VERSION
fastxtk_dir=$miniconda3_dir
# --------------- BBmap ------------------
echo ""
echo "[$(timestamp)] Installing BBmap ..."
bbmap_dir="$build_dir/bbmap/bin"
if [ -z $(check_installed $bbmap_dir) ]; then
cd $build_dir
clean "$build_dir/bbmap-${BBMAP_VERSION}"
echo "Download bbmap-v${BBMAP_VERSION}"
download $BBMAP_DOWNLOAD_URL "bbmap-${BBMAP_VERSION}.tar.gz"
tar -xzf bbmap-${BBMAP_VERSION}.tar.gz
cd bbmap
mkdir bin
cd bin
for script in $(ls ./../*.sh) ; do
s=$(basename $script)
s_pre=$(echo $s | sed 's/.sh//g')
ln -s $script $s_pre
chmod 755 $s_pre
done
cd $build_dir
rm bbmap-${BBMAP_VERSION}.tar.gz
note_installed $bbmap_dir
fi
# --------------- UCSC -----------------
ucsc_dir="$build_dir/UCSC_Utilities"
echo ""
echo "[$(timestamp)] Installing UCSC utilities ..."
if [ -z $(check_installed $ucsc_dir) ]; then
cd $build_dir
clean "$build_dir/UCSC_Utilities"
mkdir UCSC_Utilities
cd $ucsc_dir
download $BEDPARTITION_DOWNLOAD_URL "bedPartition"
download $GTFTOGENEPRED_DOWNLOAD_URL "gtfToGenePred"
download $BLAT_DOWNLOAD_URL "blat"
chmod 755 $ucsc_dir/*
note_installed $ucsc_dir
fi
# --------------- JAFFAL -----------------
jaffal_dir="$build_dir/JAFFA-version-${JAFFAL_VERSION}"
echo ""
echo "[$(timestamp)] Installing JAFFAL ..."
if [ -z $(check_installed $jaffal_dir) ]; then
cd $build_dir
download $JAFFAL_DOWNLOAD_URL "JAFFA-version-${JAFFAL_VERSION}.tar.gz"
tar xzf JAFFA-version-${JAFFAL_VERSION}.tar.gz
rm JAFFA-version-${JAFFAL_VERSION}.tar.gz
cd JAFFA-version-${JAFFAL_VERSION}
mkdir bin
g++ -std=c++11 -O3 -o ./bin/make_3_gene_fusion_table ./src/make_3_gene_fusion_table.c++
g++ -std=c++11 -O3 -o ./bin/extract_seq_from_fasta ./src/extract_seq_from_fasta.c++
g++ -std=c++11 -O3 -o ./bin/make_simple_read_table ./src/make_simple_read_table.c++
g++ -std=c++11 -O3 -o ./bin/process_transcriptome_align_table ./src/process_transcriptome_align_table.c++
g++ -O3 -o ./bin/make_count_table ./src/make_count_table.c++
echo "minimap2=\"$minimap2_dir/minimap2\"" >> tools.groovy
echo "blastn=\"$blast_dir/blastn\"" >> tools.groovy
echo "makeblastdb=\"$blast_dir/makeblastdb\"" >> tools.groovy
echo "bpipe=\"$bpipe_dir/bpipe\"" >> tools.groovy
echo "velvetg=\"$velvet_dir/velvetg\"" >> tools.groovy
echo "velveth=\"$velvet_dir/velveth\"" >> tools.groovy
echo "oases=\"$velvet_dir/oases\"" >> tools.groovy
echo "trimmomatic=\"$trimmomatic_dir/trimmomatic\"" >> tools.groovy
echo "samtools=\"$samtools_dir/samtools\"" >> tools.groovy
echo "bowtie2=\"$bowtie2_dir/bowtie2\"" >> tools.groovy
echo "blat=\"$ucsc_dir/blat\"" >> tools.groovy
echo "fasta_formatter=\"$fastxtk_dir/fasta_formatter\"" >> tools.groovy
echo "dedupe=\"$bbmap_dir/dedupe\"" >> tools.groovy
echo "reformat=\"$bbmap_dir/reformat\"" >> tools.groovy
echo "make_3_gene_fusion_table=\"$jaffal_dir/bin/make_3_gene_fusion_table\"" >> tools.groovy
echo "extract_seq_from_fasta=\"$jaffal_dir/bin/extract_seq_from_fasta\"" >> tools.groovy
echo "make_simple_read_table=\"$jaffal_dir/bin/make_simple_read_table\"" >> tools.groovy
echo "make_count_table=\"$jaffal_dir/bin/make_count_table\"" >> tools.groovy
echo "process_transcriptome_align_table=\"$jaffal_dir/bin/process_transcriptome_align_table\"" >> tools.groovy
echo "R=\"$r_path\"" >> tools.groovy
cp $jaffal_dir/known_fusions.txt $NANOTRANS_HOME/misc/human.known_fusions.txt
note_installed $jaffal_dir
fi
# --------------- Quarto -----------------
install_and_create_pkg_condaenv quarto ${QUARTO_VERSION}
echo ""
echo "#########################################################"
# Configure executable paths
cd $NANOTRANS_HOME
echo ""
echo "[$(timestamp)] All dependency instalations have finished."
echo "[$(timestamp)] Configuring executable paths ..."
echo "export NANOTRANS_HOME=${NANOTRANS_HOME}" > env.sh
echo "export build_dir=${build_dir}" >> env.sh
echo "export PYTHONPATH=${PYTHONPATH}" >> env.sh
echo "export R_LIBS=${rlib_dir}:${build_dir}/flair_conda_env/lib/R/library" >> env.sh
echo "export PERL5LIB=${PERL5LIB}" >> env.sh
echo "export cpanm_dir=${cpanm_dir}" >> env.sh
echo "export miniconda3_dir=${miniconda3_dir}" >> env.sh
#echo "export sra_dir=${sra_dir}" >> env.sh
echo "export trimmomatic_dir=${trimmomatic_dir}" >> env.sh
echo "export guppy_gpu_dir=${guppy_gpu_dir}" >> env.sh
echo "export guppy_cpu_dir=${guppy_cpu_dir}" >> env.sh
echo "export dorado_dir=${dorado_dir}" >> env.sh
echo "export nanopolish_dir=${nanopolish_dir}" >> env.sh
echo "export blast_dir=${blast_dir}" >> env.sh
# echo "export seqtk_dir=${seqtk_dir}" >> env.sh
# echo "export nanofilt_dir=${nanofilt_dir}" >> env.sh
echo "export nanoplot_dir=${nanoplot_dir}" >> env.sh
echo "export minimap2_dir=${minimap2_dir}" >> env.sh
echo "export gffread_dir=${gffread_dir}" >> env.sh
echo "export samtools_dir=${samtools_dir}" >> env.sh
echo "export bedtools_dir=${bedtools_dir}" >> env.sh
#echo "export htslib_dir=${htslib_dir}" >> env.sh
#echo "export tabix_dir=${tabix_dir}" >> env.sh
echo "export picard_dir=${picard_dir}" >> env.sh
echo "export xpore_dir=${xpore_dir}" >> env.sh
echo "export flair_dir=${flair_dir}" >> env.sh
echo "export bowtie2_dir=${bowtie2_dir}" >> env.sh
echo "export fastxtk_dir=${fastxtk_dir}" >> env.sh
echo "export bbmap_dir=${bbmap_dir}" >> env.sh
echo "export oases_dir=${oases_dir}" >> env.sh
echo "export velvet_dir=${velvet_dir}" >> env.sh
echo "export bpipe_dir=${bpipe_dir}" >> env.sh
echo "export ucsc_dir=${ucsc_dir}" >> env.sh
echo "export jaffal_dir=${jaffal_dir}" >> env.sh
echo "export quarto_dir=${build_dir}/quarto_conda_env/bin" >> env.sh
# test java configuration: requireds java 1.8
echo ""
echo "#########################################################"
echo "[$(timestamp)] Testing java configuration ..."
echo ""
java_bin=""
if type -p java
then
java_bin=$(which java)
echo "found java executable in PATH: $java_bin"
elif [[ -n "$JAVA_HOME" ]] && [[ -x "$JAVA_HOME/bin/java" ]]
then
java_bin="$JAVA_HOME/bin/java"
echo "found java executable in JAVA_HOME: $java_bin"
else
echo "";
echo "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!";
echo "Failed to detect Java installation in the system!"
echo "Please install java 1.8, which is a dependency of NanoTrans!\n";
echo "After the java installation, please manually set the directory path to java 1.8 executable on the last line of the env.sh file generated by this installation script!"
echo "export java_dir=" >> env.sh
fi
if [[ -n "$java_bin" ]]
then
java_version=$("$java_bin" -version 2>&1 | awk -F '"' '/version/ {print $2}')
echo "detected java_version: $java_version"
if [ $(tidy_version "$java_version") -eq $(tidy_version "1.8") ]
then
java_dir=$(dirname $java_bin)
echo "export java_dir=${java_dir}" >> env.sh
echo "export PATH=${java_dir}:$PATH" >> env.sh
echo "You have the correct java version for NanoTrans! NanoTrans will take care of the configuration."
else
echo "";
echo "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!";
echo "Your java version is not the version required by NanoTrans (java v1.8)!"
echo "Please manually set the directory path to java 1.8 executable on the last two lines of the env.sh file generated by this installation script!"
echo "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!";
echo "export java_dir=" >> env.sh
echo 'export PATH=${java_dir}:$PATH' >> env.sh
fi
fi
echo ""
echo "#########################################################"
# echo "[$(timestamp)] Decompress large supporting files ..."
# gunzip $NANOTRANS_HOME/data/Proteome_DB_for_annotation.CDhit_I95.fa.gz
echo "done!"
echo ""
echo ""
############################
# checking Bash exit status
if [[ $? -eq 0 ]]
then
echo "#########################################################"
echo ""
echo "[$(timestamp)] NanoTrans message: This bash script has been successfully processed! :)"
echo ""
echo "#########################################################"
echo ""
exit 0
fi
############################