PVAmplicon_install.sh

#!/bin/bash

##############################################################
##	PVAmplicon_install.sh									##
##	Creation 21/03/2019										##
##	Alexis Robitaille : robitaillea@students.iarc.fr		##
##	IARC, LYON												##
##	Last modification = 27/03/2019							##
##	Version 1.0												##
##############################################################
##	This script is used to install all the requirement to run PVAmpliconFinder tool on a Linux machine
##	For more information, please visit : https://github.com/SixEl27/PVAmpliconFinder

usage="$(basename "$0") [-h] [-p conda installation path]
This script is used to install all the requirement to run PVAmpliconFinder tool on a Linux machine.
Please note that tool installation is managed by conda, that will be installed in your system. Thus, an internet connexion is required.
All executable files will be accessible in your PATH environment variable.
If you wish to manually install the tools, please visit https://github.com/SixEl27/PVAmpliconFinder to get the complete required tool list.

Description :

    -h  show this help text
    -p	directory installation path (will be created if not already existing) - default value : PVAmpliconFinder/program\n"
    
    
while getopts ':hp:' option; do
  case "$option" in
    h) echo -e "$usage"
       exit 1
       ;;
    p) path=$OPTARG
       ;;    
    :) echo -e "$usage" >&2
	   printf "missing argument for -%s\n" "$OPTARG" >&2
       exit 1
       ;;
   \?) echo -e "$usage" >&2
	   printf "illegal option: -%s\n" "$OPTARG" >&2
       exit 1
       ;;
   (*) echo -e "$usage"
       exit 1
       ;;
   esac
done
shift $((OPTIND - 1))

if [ -z "$path" ]
then
	path="$PWD/program"
else
	mkdir -p ${path}
fi

#~ echo ${path};
#~ exit;

script_dir=$PWD;

NC='\033[0m'
BLUE='\033[0;34m'
RED='\033[0;31m'
systime=`date`
echo -e "${RED}[$systime]${NC}"
echo -e "This script will install all the requirement to run PVAmpliconFinder tool on a Linux machine."
echo -e "It may take some time, please be patient..."

echo -e "PVAmpliconFinder will be installed : ${BLUE}${path}${NC}"

##	Get the machine type
MACHINE_TYPE=`uname -m`

##	Check if Python is installed and get the Python version
PYTHON_VERSION=$(python -V 2>&1 | grep -Po '(?<=Python )(.+)')

if [[ -z "$PYTHON_VERSION" ]]
then
	PYTHON_VERSION=$(python3 -V 2>&1 | grep -Po '(?<=Python )(.+)')
fi

if [[ -z "$PYTHON_VERSION" ]]
then
    echo -e "Python is not yet installed. Please install at least Python version 2.7.0 on your machine.\n"
    echo -e "For more information, please visit : https://github.com/SixEl27/PVAmpliconFinder\n"
    exit
fi

##	Parse Python version
echo -e "Proceed installation for ${MACHINE_TYPE} machine type, using Python version ${PYTHON_VERSION}"
parsedVersion=$(echo "${PYTHON_VERSION//./}" | grep -P '^\d+' -o)


##########################
##	Conda installation	##
##########################
##	To get latest version of Miniconda, please visit https://conda.io/en/latest/miniconda.html

cd ${path}

##	Install the Miciconda version corresponding to the Phyton version installed on the system
if [[ "$parsedVersion" -lt "270" ]]										##	Python version < 2.7.0
then 
    echo -e "Python is not yet installed, or the version is too old. Please install or update your current python version."
    echo -e "For more information, please visit : https://github.com/SixEl27/PVAmpliconFinder"
    exit
elif [[ "$parsedVersion" -lt "300" && "$parsedVersion" -ge "270" ]]		##	Python version => 2.7.0 && Python version < 3.0.0
then
	echo -e "Downloading and installation of CONDA."
	if [ ${MACHINE_TYPE} == 'x86_64' ]
	then
		wget https://repo.anaconda.com/miniconda/Miniconda2-latest-Linux-x86_64.sh
		chmod +x ${path}/Miniconda2-latest-Linux-x86_64.sh
		bash ${path}/Miniconda2-latest-Linux-x86_64.sh -b -p $PWD/miniconda
		export PATH="${path}/miniconda2/bin:$PATH"
	else
		wget https://repo.anaconda.com/miniconda/Miniconda2-latest-Linux-x86.sh
		chmod +x ${path}/Miniconda2-latest-Linux-x86.sh
		bash ${path}/Miniconda2-latest-Linux-x86.sh -b -p $PWD/miniconda
		echo "${RED}Please considere that under 32bits version, you need to manually install PaPaRa"
		echo "For more information, please visit https://cme.h-its.org/exelixis/web/software/papara/index.html${NC}"
		export PATH="${path}/miniconda2/bin:$PATH"
	fi
else																	##	Python version => 3.0.0
	if [ ${MACHINE_TYPE} == 'x86_64' ]
	then
		wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
		chmod +x ${path}/Miniconda3-latest-Linux-x86_64.sh
		bash ${path}/Miniconda3-latest-Linux-x86_64.sh -b -p $PWD/miniconda
		export PATH="${path}/miniconda3/bin:$PATH"
	else
		wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86.sh
		chmod +x ${path}/Miniconda3-latest-Linux-x86.sh
		bash ${path}/Miniconda3-latest-Linux-x86.sh -b -p $PWD/miniconda
		echo "${RED}Please considere that under 32bits version, you need to manually install PaPaRa"
		echo "For more information, please visit https://cme.h-its.org/exelixis/web/software/papara/index.html${NC}"
		export PATH="${path}/miniconda3/bin:$PATH"
	fi
fi

##	Add miniconda into $PATH environment variable

#~ echo "export PATH=\"${path}/miniconda/bin:$PATH\"" >> ~/.bashrc
export PATH="${path}/miniconda/bin:$PATH"
#~ echo "export PATH=\"${path}/miniconda:$PATH\"" >> ~/.bashrc
export PATH="${path}/miniconda:$PATH"
#~ source ~/.bashrc

#~ echo ${path};
#~ echo $PATH;
#~ exit;


##	Update conda
#~ conda update -y -c defaults/label/cf201901 conda

##	Add bioconda channels
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge

##########################
##	Install the tools	##
##########################
##	All is installed with conda 

##	Tools and their dependencies
#~ conda install -y fastqc multiqc trim-galore vsearch blast raxml cap3 krona libxml2 gcc_linux-64 gxx_linux-64 gfortran_linux-64 
##	Perl packages and their dependencies
#~ conda install -y perl-padwalker perl-xml-libxml perl-libxml-perl perl-bioperl  perl-getopt-long perl-math-round perl-statistics-basic perl-list-moreutils perl-module-build perl-bioperl-run perl-text-csv

##	Evrything in once
conda install -y fastqc multiqc trim-galore vsearch blast raxml cap3 krona libxml2 gcc_linux-64 gxx_linux-64 gfortran_linux-64 perl-padwalker perl-xml-libxml perl-libxml-perl perl-bioperl perl-getopt-long perl-math-round perl-statistics-basic perl-list-moreutils perl-module-build perl-bioperl-run perl-text-csv

##	PaPaRa is not available on Conda
#~ wget https://cme.h-its.org/exelixis/resource/download/software/papara_nt-2.5-static_x86_64.tar.gz
#~ tar -xvzf papara_nt-2.5-static_x86_64.tar.gz
#~ mv $PWD/papara_static_x86_64 $PWD/papara
#~ chmod +x $PWD/papara

##	Go back to root of PVAmpliconFinder
cd ${script_dir}

##	If any issue with PaPaRa, need to be build manually : https://cme.h-its.org/exelixis/web/software/papara/index.html
#~ echo "export PATH=\"${path}:$PATH\"" >> ~/.bashrc
export PATH="${path}:$PATH"

#~ echo "export PATH=\"$PWD/program:$PATH\"" >> ~/.bashrc #For papara
export PATH="$PWD/program:$PATH"

systime=`date`
echo -e "${BLUE}Done!${NC}"
echo -e "${RED}[$systime]${NC}"

##	How to remove everything correctly
##	Everything installed with conda
#~ conda uninstall -y fastqc multiqc trim-galore vsearch blast raxml cap3 krona libxml2 gcc_linux-64 gxx_linux-64 gfortran_linux-64 perl-padwalker perl-xml-libxml perl-libxml-perl perl-bioperl  perl-getopt-long perl-math-round perl-statistics-basic perl-list-moreutils perl-module-build perl-bioperl-run perl-text-csv
##	Conda itself
#~ rm -rf $PWD/program/*

#~ Also remove the hidden .condarc file and .conda and .continuum directories which may have been created in the home directory with
source ~/.bashrc