install.sh

#! /usr/bin/env bash

<<COMMENT
This script compiles additional programs provided with Mabs.
Just run "bash install.sh" .
COMMENT

#With this command, the script stops after the first error it encounters.
set -e

#Checking that "make" is in $PATH .
if ! command -v make &> /dev/null
then
    echo 'The path to "make" is not in $PATH . Please, add it.'
    exit
fi

#Checking that "gcc" is in $PATH .
if ! command -v gcc &> /dev/null
then
    echo 'The path to "gcc" is not in $PATH . Please, add it.'
    exit
fi

#Checking that "g++" is in $PATH .
if ! command -v g++ &> /dev/null
then
    echo 'The path to "g++" is not in $PATH . Please, add it.'
    exit
fi

#Checking that "python3" is in $PATH .
if ! command -v python3 &> /dev/null
then
    echo 'The path to "python3" is not in $PATH . Please, add it.'
    exit
fi

#Checking that "perl" is in $PATH .
if ! command -v python3 &> /dev/null
then
    echo 'The path to "perl" is not in $PATH . Please, add it.'
    exit
fi

#If the user runs this script from another folder, I'm switching to the folder where this script lies.
path_to_the_folder_with_Mabs=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
cd $path_to_the_folder_with_Mabs

#Checking if the folder "Additional" exists already. If it does, deleting it. This allows Mabs to be re-installed by running install.sh
if [ -d "./Additional" ] 
then
    rm -rf ./Additional
fi

#Decompressing the archive
unzip additional.zip

#Bedtools is pre-compiled, I just change permissions.
chmod 755 ./Additional/Bedtools/bedtools

#DIAMOND is pre-compiled, I just change permissions.
chmod 755 ./Additional/DIAMOND/diamond

#Installing HMMER
cd ./Additional/HMMER
chmod 755 ./configure
./configure
make
make check
cd ../..

#MetaEuk is pre-compiled, I just change permissions. The pre-compiled version is for SSE4.1. Actually, there are MetaEuk versions for newer CPUs, but since MetaEuk is not a time-limiting step of Mabs, I don't provide them.
chmod 755 ./Additional/MetaEuk/metaeuk-linux-sse41

#Minimap2 is pre-compiled, I just change permissions.
chmod 755 ./Additional/Minimap2/minimap2

#Installing Modified_hifiasm. It is a special version of Hifiasm made for Mabs. Compared to the ordinary Hifiasm, it has an additional option "--only-primary" that forces an assembly to terminate after the GFA file with primary contigs has been made. This preliminary termination allows to save some time if only primary contigs are needed.
cd ./Additional/Modified_hifiasm
make
cd ../..

#Installing SeqTk
cd ./Additional/SeqTk
make
cd ../..

#Installing Flye
cd ./Additional/Flye
make
cd ../..

#Proovframe is written in Perl, it does not require to be compiled. I just change permissions. The source code of Proovframe was slightly modified by me — mostly for Proovframe to be able to find DIAMOND provided with Mabs.
chmod 755 ./Additional/Proovframe/bin/*

#Installing Python modules Pandas and Plotnine if they are not present.
python3 -m pip install --user Pandas
python3 -m pip install --user Plotnine

#Making mabs-hifiasm.py, mabs-flye.py and calculate_AG.py executable
chmod 755 mabs-hifiasm.py mabs-flye.py calculate_AG.py