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29/12/2021 09:06 introduction_to_microbiomics/setup_vm.sh at main · jmartinsjrbr/introduction_to_microbiomics
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#!/bin/bash
###THIS SCRIPT IS FOR INSTALLING THE NECESSARY PROGRAMS FOR OMICS COURSE ###
#@Author: Joaquim Martins Junior ###
#@Last update: 16-11-2021 ###
###OS UBUNTU 20.04 LTS 64bits###
echo "**** UPDATING SYSTEM ****"
sudo apt update && sudo apt list --upgradable && sudo apt upgrade
sudo apt install python3-pip git byobu tmux vim curl libcurl4-openssl-dev libxml2 libxm
sudo apt install openjdk-11-jdk openjdk-11-jdk-headless openjdk-11-jre-headless
#Install R
echo "**** INSTALLING R ****"
sudo apt install r-base r-base-core r-base-dev
#Set environmental vars
echo "**** SETTING ENV VARS ****"
test -d $HOME/omics_course || mkdir $HOME/omics_course
test -d $HOME/bin || mkdir $HOME/bin
test -d $HOME/omics_course/progs || mkdir $HOME/omics_course/progs
test -d $HOME/omics_course/db || mkdir $HOME/omics_course/db
##add env vars to .bashrc
echo "**** ADD PATHS TO ~/.bashrc ****"
echo "#####BIOINFORMATICS ENV VARIABLES#####" >> $HOME/.bashrc
echo "HOME_BIN=\$HOME/bin" >> $HOME/.bashrc
echo "PATH=\$HOME_BIN:\$PATH" >> $HOME/.bashrc
echo "export PATH" >> $HOME/.bashrc
source ~/.bashrc
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29/12/2021 09:06 introduction_to_microbiomics/setup_vm.sh at main · jmartinsjrbr/introduction_to_microbiomics
https://github.com/jmartinsjrbr/introduction_to_microbiomics/blob/main/setup_vm.sh 2/6
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echo "$PATH"
echo "$HOME_BIN"
###Intall Anaconda3 version 4.10.3
echo "**** INSTALLING ANACONDA3 ****"
##Dependencies:
sudo apt install libgl1-mesa-glx libegl1-mesa libxrandr2 libxrandr2 libxss1 libxcursor1
##download anaconda
cd ~/Downloads
wget https://repo.anaconda.com/archive/Anaconda3-2021.05-Linux-x86_64.sh
chmod u+x Anaconda3-2021.05-Linux-x86_64.sh
./Anaconda3-2021.05-Linux-x86_64.sh
source $HOME/omics_course/anaconda3/bin/activate
conda init
source ~/.bashrc
conda config --set auto_activate_base False
conda deactivate
###Create new anaconda environment "omics_course"
echo "**** CREATING OMICS_COURSE ENV ****"
conda update -n base -c defaults conda
conda create -n omics_course python=3.8.10
eval "$(conda shell.bash hook)"
conda activate omics_course
##install multiqc
echo "**** INSTALLING MULTIQC ****"
conda install -c bioconda -c conda-forge multiqc
##install fastp
echo "**** INSTALLING FASTP ****"
cd ~/Downloads
wget http://opengene.org/fastp/fastp
mv ./fastp ~/bin
chmod a+x ~/bin/fastp
##install sortmerna
echo "**** INSTALLING SORTMERNA ****"
conda config --add channels bioconda
conda install sortmerna
##set sortmerna databases
SORTMERNADB=$HOME/omics_course/db/sortmerna
test -d $SORTMERNADB || mkdir $SORTMERNADB
while true;
do
 read -p "Do you want to install sortmerrna databases [Yes/No]?" yn
29/12/2021 09:06 introduction_to_microbiomics/setup_vm.sh at main · jmartinsjrbr/introduction_to_microbiomics
https://github.com/jmartinsjrbr/introduction_to_microbiomics/blob/main/setup_vm.sh 3/6
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 case $yn in
 [Yy]* )
 echo "*****INSTALLING sortmerrna DB"
 cd $SORTMERNADB
 wget https://github.com/biocore/sortmerna/releases/download/v4
 tar -xvf *.tar.gz
 rm *.gz
 cd; break;;
 [Nn]* ) break;;
 esac
done
##Install o kaiju
echo "**** INSTALLING KAIJU ****"
git clone https://github.com/bioinformatics-centre/kaiju.git
cd kaiju/src
make
cd ../../
mv kaiju* $HOME/omics_course/progs
echo -e "\n##KAIJU SETUP" >> ~/.bashrc
echo "export PATH=\$HOME/omics_course/progs/kaiju/bin/:\$PATH" >> ~/.bashrc
##set kaiju databases (nr_euk)
KAIJUDB=$HOME/omics_course/db/kaiju
test -d $KAIJUDB || mkdir $KAIJUDB
SELECTED_DB='nr_euk'
while true;
do
 read -p "Do you want to install KAIJU nr_euk databases [Yes/No]?" yn
 case $yn in
 [Yy]* )
 echo "*****INSTALLING KAIJU (nr_euk) DB"
 cd $KAIJUDB
 kaiju-makedb -s $SELECTED_DB
 cd; break;;
 [Nn]* ) break;;
 esac
done
##Install KronaTools
echo "**** INSTALLING KRONATOOLS ****"
cd ~/Downloads
wget https://github.com/marbl/Krona/releases/download/v2.8/KronaTools-2.8.tar
mkdir $HOME/omics_course/progs/KronaTools-2.8
tar -xvf KronaTools-2.8.tar
rm -rf KronaTools-2.8.tar
mv KronaTools-2.8 $HOME/omics_course/progs/
cd $HOME/omics_course/progs/KronaTools-2.8
chmod u+x ./install.pl
sudo ./install.pl
29/12/2021 09:06 introduction_to_microbiomics/setup_vm.sh at main · jmartinsjrbr/introduction_to_microbiomics
https://github.com/jmartinsjrbr/introduction_to_microbiomics/blob/main/setup_vm.sh 4/6
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##install spades
echo "**** INSTALLING SPADES ****"
conda install -c bioconda spades
##Install kallisto
echo "**** INSTALLING KALLISTO ****"
conda install -c bioconda kallisto
conda deactivate
#Install prokka
echo "**** INSTALLING PROKKA ****"
conda create -n prokka -c conda-forge -c bioconda -c defaults prokka
#Install run_dbcan
echo "**** INSTALLING DBCAN ****"
conda create -n run_dbcan python=3.8 diamond hmmer prodigal -c conda-forge -c bioconda
conda activate run_dbcan
pip3 install run-dbcan==2.0.11
cd $HOME/omics_course/db
test -d dbcan || mkdir $HOME/omics_course/db/dbcan
cd $HOME/omics_course/db/dbcan
wget https://bcb.unl.edu/dbCAN2/download/CAZyDB.09242021.fa && diamond makedb --in CAZy
wget https://bcb.unl.edu/dbCAN2/download/dbCAN-HMMdb-V10.txt && mv dbCAN-HMMdb-V10.txt 
wget http://bcb.unl.edu/dbCAN2/download/Databases/tcdb.fa && diamond makedb --in tcdb.f
wget http://bcb.unl.edu/dbCAN2/download/Databases/tf-1.hmm && hmmpress tf-1.hmm
wget http://bcb.unl.edu/dbCAN2/download/Databases/tf-2.hmm && hmmpress tf-2.hmm
wget http://bcb.unl.edu/dbCAN2/download/Databases/stp.hmm && hmmpress stp.hmm
conda deactivate
##install metawrap
echo "**** INSTALLING METAWRAP ****"
#download metawrap
cd $HOME/omics_course
test -d progs ||mkdir $HOME/omics_course/progs
cd $HOME/omics_course/progs
git clone https://github.com/bxlab/metaWRAP.git
echo -e "\n##METAWRAPSETUP" >> ~/.bashrc
echo "export PATH=\$HOME/omics_course/progs/metaWRAP/bin/:\$PATH" >> ~/.bashrc
#Create metawrap env
conda create -y -n metawrap-env python=2.7
conda activate metawrap-env
#install dependencies
conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda
conda config --add channels ursky
conda install --only-deps -c ursky metawrap-mg
#Set quast databases
29/12/2021 09:06 introduction_to_microbiomics/setup_vm.sh at main · jmartinsjrbr/introduction_to_microbiomics
https://github.com/jmartinsjrbr/introduction_to_microbiomics/blob/main/setup_vm.sh 5/6
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quast-download-gridss
quast-download-silva
quast-download-busco
ktUpdateTaxonomy.sh
###Manually download buscodb in case failing in previous attempt
BUSCODBDIR=/home/bioinfo/omics_course/anaconda3/envs/metawrap-env/lib/python2.7/site-pa
while true;
do
 read -p "Do you want to install BUSCO DB for metawrap (Quast) manually [Yes/No]
 case $yn in
 [Yy]* )
 echo "*****INSTALLING BUSCO DBs (Quast) manually"
 cd $BUSCODBDIR
 echo "*****Downloading bacteria db..."
 wget https://busco.ezlab.org/v2/datasets/bacteria_odb9.tar.gz
 tar -vzxf *.tar.gz
 echo "*****Downloading eukaryota db..."
 wget https://busco.ezlab.org/v2/datasets/eukaryota_odb9.tar.gz
 tar -vzxf eukaryota_odb9.tar.gz
 echo "*****Downloading fungi db..."
 wget https://busco.ezlab.org/v2/datasets/fungi_odb9.tar.gz
 tar -vzxf fungi_odb9.tar.gz
 cd; break;;
 [Nn]* ) break;;
 esac
done
cd
####### INSTALL METAWRAP DATABASES #####
METAWRAP_MAIN_DBDIR=$HOME/omics_course/db/metawrap
CHECKM_FOLDER=$METAWRAP_MAIN_DBDIR/checkm
KRAKEN2DB=$METAWRAP_MAIN_DBDIR/kraken2
NCBI_NT=$METAWRAP_MAIN_DBDIR/ncbi/nt
NCBI_tax=$METAWRAP_MAIN_DBDIR/ncbi/taxonomy
BMTAGGER=$METAWRAP_MAIN_DBDIR/bmtagger
test -d $METAWRAP_MAIN_DBDIR || mkdir $METAWRAP_MAIN_DBDIR
test -d $CHECKM_FOLDER || mkdir $CHECKM_FOLDER
test -d $KRAKEN2DB || mkdir $KRAKEN2DB
test -d $NCBI_NT || mkdir -p $NCBI_NT
test -d $BMTAGGER || mkdir $BMTAGGER
test -d $NCBI_tax || mkdir -p $NCBI_tax
while true;
29/12/2021 09:06 introduction_to_microbiomics/setup_vm.sh at main · jmartinsjrbr/introduction_to_microbiomics
https://github.com/jmartinsjrbr/introduction_to_microbiomics/blob/main/setup_vm.sh 6/6
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do
 read -p "Do you want to install metaWRAP databases [Yes/No]?" yn
 case $yn in
 [Yy]* )
 echo "*****INSTALLING CHECKM DB"
 cd $CHECKM_FOLDER
 wget https://data.ace.uq.edu.au/public/CheckM_databases/checkm_
 tar -xvf *.tar.gz
 rm *.gz
 cd ../
 echo "*****INSTALLING KRAKEN2 DB"
 cd $KRAKEN2DB
 kraken2-build --standard --threads 10 --db $KRAKEN2DB
 echo "Do not forget to set the KRAKEN_DB variable in the config
 cd ../
 echo "*****INSTALLING NCBI_nt BLAST databases"
 cd $NCBI_NT
 wget "ftp://ftp.ncbi.nlm.nih.gov/blast/db/nt.*.tar.gz"
 for a in nt.*.tar.gz; do tar xzf $a; done
 echo "Do not forget to set the BLASTDB variable in the config-m
 cd ../
 echo "*****INSTALLING NCBI TAXONOMY"
 cd $NCBI_tax
 wget ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz
 tar -xvf taxdump.tar.gz
 echo "Do not forget to set the TAXDUMP variable in the config-m
 cd ../
 echo "Access the link below to make host genome index for bmtag
 echo "https://github.com/bxlab/metaWRAP/blob/master/installatio
 cd ; break;;
 [Nn]* ) exit;;
 esac
done
#Install SAMSA2
cd $HOME/omics_course/progs
git clone https://github.com/transcript/samsa2.git
SAMSA2DIR=$HOME/omics_course/progs/samsa2
test -d $SAMSA2DIR || mkdir $SAMSA2DIR
cd $SAMSA2DIR/setup_and_test
chmod u+x package_installation.bash
sed -i 's/install_packages.R/install_packages_R_3.6.R/g' package_installation.bash
./package_installation.bash