NanoCLUST_test_Centos7.sh

#!/bin/bash

###################################################################
#Script Name	: Nanoclust Demo
#Description	: NanoCLUST installation test for Centos 7                                                  
#Author       	: Arup Ghosh
#Web         	: https://arup.dev
###################################################################

set -e

if groups $(whoami)| grep -q '\bdocker\b'; then
    printf "User $(whoami) present in docker\nStarting the run\n\n"
else
    printf "Add $(whoami) in docker group"
    exit 1
fi


#get timestamp for foldername
timestamp=$(date +%s)

mkdir nct_${timestamp} && cd nct_${timestamp}

wait
printf "Folder created\n\n"

#clone the repo 
git clone https://github.com/genomicsITER/NanoCLUST.git

printf "Repo cloned successfully\n\n"

#download and expand the blast db files
mkdir NanoCLUST/db NanoCLUST/db/taxdb
wget -4 https://ftp.ncbi.nlm.nih.gov/blast/db/16S_ribosomal_RNA.tar.gz
wget -4 https://ftp.ncbi.nlm.nih.gov/blast/db/16S_ribosomal_RNA.tar.gz.md5
wget -4 https://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz
wget -4 https://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz.md5
wait
cat *.md5| md5sum -c 
wait
tar -xzvf 16S_ribosomal_RNA.tar.gz -C NanoCLUST/db
tar -xzvf taxdb.tar.gz -C NanoCLUST/db/taxdb

printf "Blast database downloaded successfully\n\n"

#download current version of nextflow
wget -4 https://github.com/nextflow-io/nextflow/releases/download/v21.04.1/nextflow-21.04.1-all && mv nextflow-21.04.1-all nextflow
wait
chmod a+x nextflow

#perform a test run to make sure installation is working fine
./nextflow run NanoCLUST/main.nf -profile test,docker --db "db/16S_ribosomal_RNA" --tax "db/taxdb/"