install_bootable.sh

#!bin/bash

#!/bin/bash

progress_bar() {
  local duration
  local columns
  local space_available
  local fit_to_screen
  local space_reserved

  space_reserved=6   # reserved width for the percentage value
  duration=${1}
  columns=$(tput cols)
  space_available=$(( columns-space_reserved ))
  elapsed=${2}

  if (( duration < space_available )); then
        fit_to_screen=1;
  else
    fit_to_screen=$(( duration / space_available ));
    fit_to_screen=$((fit_to_screen+1));
  fi

  already_done() { for ((done=0; done<(elapsed / fit_to_screen) ; done=done+1 )); do printf "▇"; done }
  remaining() { for (( remain=(elapsed/fit_to_screen) ; remain<(duration/fit_to_screen) ; remain=remain+1 )); do printf " "; done }
  percentage() { echo -n "| $duration% "; }
  clean_line() { printf "\r"; }

  for (( elapsed; elapsed<=duration; elapsed=elapsed+1 )); do
      already_done; remaining; percentage
      clean_line
  done
  clean_line
}

# Create empty directories

progress_bar 0 0

if [ -d log ]
then
        echo "Directory log already exists."
else
        mkdir log
fi

if [ -d benchmark_output ]
then
        echo "Directory benchmark_output already exists."
else
        mkdir benchmark_output
fi

if [ -d benchmark_output/BBMap ]
then
        echo "Directory benchmark_output/BBMap already exists."
else
	mkdir benchmark_output/BBMap
fi

if [ -d benchmark_output/bowtie2 ]
then
        echo "Directory benchmark_output/bowtie2 already exists."
else
	mkdir benchmark_output/bowtie2
fi

if [ -d benchmark_output/BWA ]
then
        echo "Directory benchmark_output/BWA already exists."
else
        mkdir benchmark_output/BWA
fi

if [ -d benchmark_output/clustalOmega ]
then
        echo "Directory benchmark_output/clustalOmega already exists."
else
	mkdir benchmark_output/clustalOmega
fi

if [ -d benchmark_output/gromacs ]
then
        echo "Directory benchmark_output/gromacs already exists."
else
	mkdir benchmark_output/gromacs
fi

if [ -d benchmark_output/IDBA ]
then
        echo "Directory benchmark_output/IDBA already exists."
else
	mkdir benchmark_output/IDBA
fi

if [ -d benchmark_output/MAFFT ]
then
        echo "Directory benchmark_output/MAFFT already exists."
else
        mkdir benchmark_output/MAFFT
fi

if [ -d benchmark_output/SINA ]
then
        echo "Directory benchmark_output/SINA already exists."
else
        mkdir benchmark_output/SINA
fi

if [ -d benchmark_output/SPAdes ]
then
        echo "Directory benchmark_output/SPAdes already exists."
else
	mkdir benchmark_output/SPAdes
fi

if [ -d benchmark_output/tensorflow ]
then
        echo "Directory benchmark_output/tensorflow already exists."
else
	mkdir benchmark_output/tensorflow
fi

if [ -d benchmark_output/velvet ]
then
        echo "Directory benchmark_output/velvet already exists."
else
	mkdir benchmark_output/velvet
fi

if [ -d datasets ]
then
        echo "Directory datasets already exists."
else
	mkdir datasets
fi

if [ -d datasets/1000_genomes ]
then
        echo "Directory datasets/1000_genomes already exists."
else
	mkdir datasets/1000_genomes
fi

if [ -d datasets/BWA ]
then
        echo "Directory datasets/BWA already exists."
else
        mkdir datasets/BWA
fi

if [ -d datasets/BWA/DRR001012/ ]
then
        echo "Directory datasets/BWA/DRR001012/ already exists."
else
        mkdir datasets/BWA/DRR001012/
fi

if [ -d datasets/BWA/DRR001025/ ]
then
        echo "Directory datasets/BWA/DRR001025/ already exists."
else
        mkdir datasets/BWA/DRR001025/
fi

if [ -d datasets/BWA//GRCh38_full_analysis_set_plus_decoy_hla/ ]
then
        echo "Directory datasets/BWA//GRCh38_full_analysis_set_plus_decoy_hla/ already exists."
else
        mkdir datasets/BWA//GRCh38_full_analysis_set_plus_decoy_hla/
fi

if [ -d datasets/clustalOmega ]
then
        echo "Directory datasets/clustalOmega already exists."
else
	mkdir datasets/clustalOmega
fi

if [ -d datasets/gromacs ]
then
        echo "Directory datasets/gromacs already exists."
else
	mkdir datasets/gromacs
fi

if [ -d datasets/SINA ]
then
        echo "Directory datasets/SINA already exists."
else
        mkdir datasets/SINA
fi

if [ -d datasets/tensorflow ]
then
        echo "Directory datasets/tensorflow already exists."
else
	mkdir datasets/tensorflow
fi

if [ -d datasets/ebi ]
then
        echo "Directory datasets/ebi already exists."
else
	mkdir datasets/ebi
fi

if [ -d backed_up_benchmark_results ]
then
        echo "Directory backed_up_benchmark_results already exists."
else
	mkdir backed_up_benchmark_results
fi

if [ -d gromacs ]
then
        echo "Directory gromacs already exists."
else
	mkdir gromacs
fi

if [ -d results ]
then
        echo "Directory results already exists."
else
	mkdir results
fi

if [ -d BBMap ]
then
        echo "Directory BBMap already exists."
else
        mkdir BBMap
fi

if [ -d bowtie2 ]
then
        echo "Directory bowtie2 already exists."
else
	mkdir bowtie2
fi

if [ -d BWA ]
then
        echo "Directory BWA already exists."
else
        mkdir BWA
fi

if [ -d clustalOmega ]
then
        echo "Directory clustalOmega already exists."
else
	mkdir clustalOmega
fi

if [ -d IDBA ]
then
        echo "Directory IDBA already exists."
else
	mkdir IDBA
fi

if [ -d MAFFT ]
then
        echo "Directory MAFFT already exists."
else
        mkdir MAFFT
fi

if [ -d SINA ]
then
        echo "Directory SINA already exists."
else
        mkdir SINA
fi

if [ -d SPAdes ]
then
        echo "Directory SPAdes already exists."
else
	mkdir SPAdes
fi

if [ -d tensorflow ]
then
        echo "Directory tensorflow already exists."
else
	mkdir tensorflow
fi

if [ -d velvet ]
then
        echo "Directory velvet already exists."
else
	mkdir velvet
fi

if [ -d gcc ]
then
        echo "Directory gcc already exists."
else
	mkdir gcc
fi

if [ -d gcc/gcc-build ]
then
        echo "Directory gcc/gcc-build already exists."
else
	mkdir gcc/gcc-build
fi

if [ -d gcc/gcc-installed ]
then
        echo "Directory gcc/gcc-installed already exists."
else
	mkdir gcc/gcc-installed
fi

if [ -d nmon_stats ]
then
        echo "Directory nmon_stats already exists."
else
	mkdir nmon_stats
fi

progress_bar 1 0

# Download benchmark datasets

if [ -e datasets/1000_genomes/ERR251006.filt.fastq ]
then
	echo "File datasets/1000_genomes/ERR251006.filt.fastq already exists."
else
	#wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG00110/sequence_read/ERR251006.filt.fastq.gz -P datasets/1000_genomes/
	wget https://s3.denbi.uni-tuebingen.de/max/ERR251006.filt.fastq.gz -P datasets/1000_genomes/ >>log/dataset_ERR251006.log 2>&1
	gunzip datasets/1000_genomes/ERR251006.filt.fastq.gz >>log/dataset_ERR251006.log 2>&1
fi

if [ -e datasets/1000_genomes/ERR016155.filt.fastq ]
then
	echo "File datasets/1000_genomes/ERR016155.filt.fastq already exists."
else
	#wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG00125/sequence_read/ERR016155.filt.fastq.gz -P datasets/1000_genomes/
	wget https://s3.denbi.uni-tuebingen.de/max/ERR016155.filt.fastq.gz -P datasets/1000_genomes/ >>log/dataset_ERR016155.log 2>&1
	gunzip datasets/1000_genomes/ERR016155.filt.fastq.gz >>log/dataset_ERR016155.log 2>&1
fi

if [ -e datasets/1000_genomes/ERR015528.filt.fastq ]
then
        echo "File datasets/1000_genomes/ERR015528.filt.fastq already exists."
else
        #wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG00106/sequence_read/ERR015528.filt.fastq.gz -P datasets/1000_genomes/
        wget https://s3.denbi.uni-tuebingen.de/max/ERR015528.filt.fastq.gz -P datasets/1000_genomes/ >>log/dataset_ERR015528.log 2>&1
        gunzip datasets/1000_genomes/ERR015528.filt.fastq.gz >>log/dataset_ERR015528.log 2>&1
fi

if [ -e datasets/1000_genomes/SRR741411.filt.fastq ]
then
        echo "File datasets/1000_genomes/SRR741411.filt.fastq already exists."
else
        #wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG00099/sequence_read/SRR741411.filt.fastq.gz -P datasets/1000_genomes/
        wget https://s3.denbi.uni-tuebingen.de/max/SRR741411.filt.fastq.gz -P datasets/1000_genomes/ >>log/dataset_SRR741411.log 2>&1
        gunzip datasets/1000_genomes/SRR741411.filt.fastq.gz >>log/dataset_SRR741411.log 2>&1
fi

if [ -e datasets/ebi/DRR001012.fastq ]
then
        echo "File datasets/ebi/DRR001012.fastq already exists."
else
	#wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/DRR001/DRR001012/DRR001012.fastq.gz -P datasets/ebi/
	wget https://s3.denbi.uni-tuebingen.de/max/DRR001012.fastq.gz -P datasets/ebi/ >>log/dataset_DRR001012.log 2>&1
	gunzip datasets/ebi/DRR001012.fastq.gz >>log/dataset_DRR001012.log 2>&1
fi

if [ -e datasets/ebi/DRR001025.fastq ]
then
        echo "File datasets/ebi/DRR001025.fastq already exists."
else
	#wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/DRR001/DRR001025/DRR001025.fastq.gz -P datasets/ebi/
	wget https://s3.denbi.uni-tuebingen.de/max/DRR001025.fastq.gz -P datasets/ebi/ >>log/dataset_DRR001025.log 2>&1
	gunzip datasets/ebi/DRR001025.fastq.gz >>log/dataset_DRR001025.log 2>&1
fi

if [ -e datasets/1000_genomes/GRCh38_full_analysis_set_plus_decoy_hla.fa ]
then
        echo "File datasets/1000_genomes/GRCh38_full_analysis_set_plus_decoy_hla.fa already exists."
else
	#wget http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/GRCh38_reference_genome/GRCh38_full_analysis_set_plus_decoy_hla.fa -P datasets/1000_genomes/
	wget https://s3.denbi.uni-tuebingen.de/max/GRCh38_full_analysis_set_plus_decoy_hla.fa -P datasets/1000_genomes/ >>log/dataset_GRCh38_full_analysis_set_plus_decoy_hla.log 2>&1
fi

if [ -e datasets/BWA/DRR001012/DRR001012.amb ]
then
        echo "File datasets/BWA/DRR001012/DRR001012.amb already exists."
else
        wget https://s3.denbi.uni-tuebingen.de/max/DRR001012.amb -P datasets/BWA/DRR001012/ >>log/dataset_BWA_DRR001012_amb.log 2>&1
fi

if [ -e datasets/BWA/DRR001012/DRR001012.ann ]
then
        echo "File datasets/BWA/DRR001012/DRR001012.ann already exists."
else
        wget https://s3.denbi.uni-tuebingen.de/max/DRR001012.ann -P datasets/BWA/DRR001012/ >>log/dataset_BWA_DRR001012_ann.log 2>&1
fi

if [ -e datasets/BWA/DRR001012/DRR001012.bwt ]
then
        echo "File datasets/BWA/DRR001012/DRR001012.bwt already exists."
else
        wget https://s3.denbi.uni-tuebingen.de/max/DRR001012.bwt -P datasets/BWA/DRR001012/ >>log/dataset_BWA_DRR001012_bwt.log 2>&1
fi

if [ -e datasets/BWA/DRR001012/DRR001012.pac ]
then
        echo "File datasets/BWA/DRR001012/DRR001012.pac already exists."
else
        wget https://s3.denbi.uni-tuebingen.de/max/DRR001012.pac -P datasets/BWA/DRR001012/ >>log/dataset_BWA_DRR001012_pac.log 2>&1
fi

if [ -e datasets/BWA/DRR001012/DRR001012.sa ]
then
        echo "File datasets/BWA/DRR001012/DRR001012.sa already exists."
else
        wget https://s3.denbi.uni-tuebingen.de/max/DRR001012.sa -P datasets/BWA/DRR001012/ >>log/dataset_BWA_DRR001012_sa.log 2>&1
fi

if [ -e datasets/BWA/DRR001025/DRR001025.amb ]
then
        echo "File datasets/BWA/DRR001025/DRR001025.amb already exists."
else
        wget https://s3.denbi.uni-tuebingen.de/max/DRR001025.amb -P datasets/BWA/DRR001025/ >>log/dataset_BWA_DRR001025_amb.log 2>&1
fi

if [ -e datasets/BWA/DRR001025/DRR001025.ann ]
then
        echo "File datasets/BWA/DRR001025/DRR001025.ann already exists."
else
        wget https://s3.denbi.uni-tuebingen.de/max/DRR001025.ann -P datasets/BWA/DRR001025/ >>log/dataset_BWA_DRR001025_ann.log 2>&1
fi

if [ -e datasets/BWA/DRR001025/DRR001025.bwt ]
then
        echo "File datasets/BWA/DRR001025/DRR001025.bwt already exists."
else
        wget https://s3.denbi.uni-tuebingen.de/max/DRR001025.bwt -P datasets/BWA/DRR001025/ >>log/dataset_BWA_DRR001025_bwt.log 2>&1
fi

if [ -e datasets/BWA/DRR001025/DRR001025.pac ]
then
        echo "File datasets/BWA/DRR001025/DRR001025.pac already exists."
else
        wget https://s3.denbi.uni-tuebingen.de/max/DRR001025.pac -P datasets/BWA/DRR001025/ >>log/dataset_BWA_DRR001025_pac.log 2>&1
fi

if [ -e datasets/BWA/DRR001025/DRR001025.sa ]
then
        echo "File datasets/BWA/DRR001025/DRR001025.sa already exists."
else
        wget https://s3.denbi.uni-tuebingen.de/max/DRR001025.sa -P datasets/BWA/DRR001025/ >>log/dataset_BWA_DRR001025_sa.log 2>&1
fi

if [ -e datasets/BWA/GRCh38_full_analysis_set_plus_decoy_hla/GRCh38_full_analysis_set_plus_decoy_hla.amb ]
then
        echo "File datasets/BWA/GRCh38_full_analysis_set_plus_decoy_hla/GRCh38_full_analysis_set_plus_decoy_hla.amb already exists."
else
        wget https://s3.denbi.uni-tuebingen.de/max/GRCh38_full_analysis_set_plus_decoy_hla.amb -P datasets/BWA/GRCh38_full_analysis_set_plus_decoy_hla/ >>log/dataset_BWA_GRCh38_full_analysis_set_plus_decoy_hla_amb.log 2>&1
fi

if [ -e datasets/BWA/GRCh38_full_analysis_set_plus_decoy_hla/GRCh38_full_analysis_set_plus_decoy_hla.ann ]
then
        echo "File datasets/BWA/GRCh38_full_analysis_set_plus_decoy_hla/GRCh38_full_analysis_set_plus_decoy_hla.ann already exists."
else
        wget https://s3.denbi.uni-tuebingen.de/max/GRCh38_full_analysis_set_plus_decoy_hla.ann -P datasets/BWA/GRCh38_full_analysis_set_plus_decoy_hla/ >>log/dataset_BWA_GRCh38_full_analysis_set_plus_decoy_hla_ann.log 2>&1
fi

if [ -e datasets/BWA/GRCh38_full_analysis_set_plus_decoy_hla/GRCh38_full_analysis_set_plus_decoy_hla.bwt ]
then
        echo "File datasets/BWA/GRCh38_full_analysis_set_plus_decoy_hla/GRCh38_full_analysis_set_plus_decoy_hla.bwt already exists."
else
        wget https://s3.denbi.uni-tuebingen.de/max/GRCh38_full_analysis_set_plus_decoy_hla.bwt -P datasets/BWA/GRCh38_full_analysis_set_plus_decoy_hla/ >>log/dataset_BWA_GRCh38_full_analysis_set_plus_decoy_hla_bwt.log 2>&1
fi

if [ -e datasets/BWA/GRCh38_full_analysis_set_plus_decoy_hla/GRCh38_full_analysis_set_plus_decoy_hla.pac ]
then
        echo "File datasets/BWA/GRCh38_full_analysis_set_plus_decoy_hla/GRCh38_full_analysis_set_plus_decoy_hla.pac already exists."
else
        wget https://s3.denbi.uni-tuebingen.de/max/GRCh38_full_analysis_set_plus_decoy_hla.pac -P datasets/BWA/GRCh38_full_analysis_set_plus_decoy_hla/ >>log/dataset_BWA_GRCh38_full_analysis_set_plus_decoy_hla_pac.log 2>&1
fi

if [ -e datasets/BWA/GRCh38_full_analysis_set_plus_decoy_hla/GRCh38_full_analysis_set_plus_decoy_hla.sa ]
then
        echo "File datasets/BWA/GRCh38_full_analysis_set_plus_decoy_hla/GRCh38_full_analysis_set_plus_decoy_hla.sa already exists."
else
        wget https://s3.denbi.uni-tuebingen.de/max/GRCh38_full_analysis_set_plus_decoy_hla.sa -P datasets/BWA/GRCh38_full_analysis_set_plus_decoy_hla/ >>log/dataset_BWA_GRCh38_full_analysis_set_plus_decoy_hla_sa.log 2>&1
fi

if [ -e datasets/clustalOmega/wgs.ANCA.1_200.fsa ]
then
        echo "File datasets/clustalOmega/wgs.ANCA.1_200.fsa already exists."
else
        wget https://s3.denbi.uni-tuebingen.de/max/wgs.ANCA.1_200.fsa -P datasets/clustalOmega >>log/dataset_wgs.ANCA.1_200.log 2>&1
fi


if [ -e datasets/clustalOmega/wgs.ANCA.1_400.fsa ]
then
        echo "File datasets/clustalOmega/wgs.ANCA.1_400.fsa already exists."
else
        wget https://s3.denbi.uni-tuebingen.de/max/wgs.ANCA.1_400.fsa -P datasets/clustalOmega >>log/dataset_wgs.ANCA.1_400.log 2>&1
fi


if [ -e datasets/clustalOmega/wgs.ANCA.1_500.fsa ]
then
        echo "File datasets/clustalOmega/wgs.ANCA.1_500.fsa already exists."
else
	wget https://s3.denbi.uni-tuebingen.de/max/wgs.ANCA.1_500.fsa -P datasets/clustalOmega >>log/dataset_wgs.ANCA.1_500.log 2>&1
fi


if [ -d datasets/tensorflow/cifar-10-batches-bin ]
then
	echo "Directory datasets/tensorflow/cifar-10-batches-bin already exists."
else	
	wget https://s3.denbi.uni-tuebingen.de/max/cifar-10-binary.tar.gz -P datasets/tensorflow >>log/dataset_cifar-10-batches-bin.log 2>&1
	tar -xf datasets/tensorflow/cifar-10-binary.tar.gz -C datasets/tensorflow/ >>log/dataset_cifar-10-batches-bin.log 2>&1
fi

if [ -d datasets/tensorflow/models ]
then
        echo "Directory datasets/tensorflow/models already exists."
else    
	wget https://s3.denbi.uni-tuebingen.de/max/models.tar.gz -P datasets/tensorflow >>log/dataset_tensorflow_models.log 2>&1
	tar -xf datasets/tensorflow/models.tar.gz -C datasets/tensorflow/ >>log/dataset_tensorflow_models.log 2>&1
	rm datasets/tensorflow/models.tar.gz >>log/dataset_tensorflow_models.log 2>&1
fi

if [ -e datasets/SINA/SILVA_138.1_SSURef_NR99_12_06_20_opt.arb ]
then
        echo "File datasets/SINA/SILVA_138.1_SSURef_NR99_12_06_20_opt.arb already exists."
else
	#wget https://www.arb-silva.de/fileadmin/arb_web_db/release_138_1/ARB_files/SILVA_138.1_SSURef_NR99_12_06_20_opt.arb.gz
        wget https://s3.denbi.uni-tuebingen.de/max/SILVA_138.1_SSURef_NR99_12_06_20_opt.arb.gz -P datasets/SINA/ >>log/dataset_SINA_SILVA_138.1_SSURef_NR99_12_06_20_opt.arb.log 2>&1
	gunzip datasets/SINA/SILVA_138.1_SSURef_NR99_12_06_20_opt.arb.gz >>log/dataset_SINA_SILVA_138.1_SSURef_NR99_12_06_20_opt.arb.log 2>&1
fi

if [ -e datasets/SINA/SILVA_138.1_SSURef_NR99_12_06_20_opt.sidx ]
then
        echo "File datasets/SINA/SILVA_138.1_SSURef_NR99_12_06_20_opt.sidx already exists."
else
        wget https://s3.denbi.uni-tuebingen.de/max/SILVA_138.1_SSURef_NR99_12_06_20_opt.sidx -P datasets/SINA/ >>log/dataset_SINA_SILVA_138.1_SSURef_NR99_12_06_20_opt.sidx.log 2>&1
fi

if [ -e datasets/SINA/GTDB_bac-arc_ssu_r86.fa ]
then
        echo "File datasets/SINA/GTDB_bac-arc_ssu_r86.fa already exists."
else 
	#wget https://zenodo.org/record/2541239/files/GTDB_bac-arc_ssu_r86.fa.gz
        wget https://s3.denbi.uni-tuebingen.de/max/GTDB_bac-arc_ssu_r86.fa.gz -P datasets/SINA/ >>log/dataset_SINA_GTDB_bac-arc_ssu_r86.log 2>&1
	gunzip datasets/SINA/GTDB_bac-arc_ssu_r86.fa.gz >>log/dataset_SINA_GTDB_bac-arc_ssu_r86.log 2>&1
fi

if [ -e datasets/SINA/RefSeq-RDP16S_v2_May2018.fa ]
then
        echo "File datasets/SINA/RefSeq-RDP16S_v2_May2018.fa already exists."
else
        #wget https://zenodo.org/record/2541239/files/RefSeq-RDP16S_v2_May2018.fa.gz
        wget https://s3.denbi.uni-tuebingen.de/max/RefSeq-RDP16S_v2_May2018.fa.gz -P datasets/SINA/ >>log/dataset_SINA_RefSeq-RDP16S_v2_May2018.log 2>&1
        gunzip datasets/SINA/RefSeq-RDP16S_v2_May2018.fa.gz >>log/dataset_SINA_RefSeq-RDP16S_v2_May2018.log 2>&1
fi

if [ -e datasets/SINA/OE-38_R1.fastq ]
then
        echo "File datasets/SINA/OE-38_R1.fastq already exists."
else
        #wget https://zenodo.org/record/803376/files/OE-38_R1.fastq.gz
        wget https://s3.denbi.uni-tuebingen.de/max/OE-38_R1.fastq.gz -P datasets/SINA/ >>log/dataset_SINA_OE-38_R1.log 2>&1
        gunzip datasets/SINA/OE-38_R1.fastq.gz >>log/dataset_SINA_OE-38_R1.log 2>&1
fi

if [ -d datasets/gromacs/adh_cubic ]
then
        echo "Directory datasets/gromacs/adh_cubic already exists."
else
	wget https://s3.denbi.uni-tuebingen.de/max/ADH_bench_systems.tar.gz -P datasets/gromacs >>log/dataset_gromacs_adh_cubic.log 2>&1
	tar -xf datasets/gromacs/ADH_bench_systems.tar.gz -C datasets/gromacs/ >>log/dataset_gromacs_adh_cubic.log 2>&1
	rm datasets/gromacs/ADH_bench_systems.tar.gz >>log/dataset_gromacs_adh_cubic.log 2>&1
fi

progress_bar 8 1

# Download GCC compiler version 7.3.0
if [ -d gcc/gcc-7.3.0 ]
then
	echo "Directory gcc/gcc-7.3.0 already exists."
else
	wget https://s3.denbi.uni-tuebingen.de/max/gcc-7.3.0.tar.gz -P gcc >>log/download_gcc.log 2>&1
	tar -xf gcc/gcc-7.3.0.tar.gz -C gcc/ >>log/download_gcc.log 2>&1
	rm gcc/gcc-7.3.0.tar.gz >>log/download_gcc.log 2>&1
fi

# Download nmonchart34
if ! [ -d nmonchart ]
then
	wget https://s3.denbi.uni-tuebingen.de/max/nmonchart34.tar >>log/download_nmonchart34.log 2>&1
	tar -xf nmonchart34.tar >>log/download_nmonchart34.log 2>&1
	rm nmonchart34.tar >>log/download_nmonchart34.log 2>&1
else
	echo "Directory nmonchart already exist."
fi

# Download BBMap binaries
if [ -d BBMap/bbmap ]
then
        echo "Directory BBMap/bbmap already exists."
else
        wget https://s3.denbi.uni-tuebingen.de/max/BBMap_38.87.tar.gz -P BBMap >>log/download_BBMap.log 2>&1
        tar -xf BBMap/BBMap_38.87.tar.gz -C BBMap/ >>log/download_BBMap.log 2>&1
        rm BBMap/BBMap_38.87.tar.gz >>log/download_BBMap.log 2>&1
fi

# Download Bowtie2 sources
if [ -d bowtie2/bowtie2-2.4.2 ]
then
        echo "Directory bowtie2/bowtie2-2.4.2 already exists."
else
	wget https://s3.denbi.uni-tuebingen.de/max/bowtie2-2.4.2-source.zip -P bowtie2 >>log/download_bowtie2.log 2>&1
	unzip bowtie2/bowtie2-2.4.2-source.zip -d bowtie2/ >>log/download_bowtie2.log 2>&1
	rm bowtie2/bowtie2-2.4.2-source.zip >>log/download_bowtie2.log 2>&1
fi

# Download BWA sources
if [ -d BWA/bwa-0.7.17 ]
then
        echo "Directory BWA/bwa-0.7.17 already exists."
else
        wget https://s3.denbi.uni-tuebingen.de/max/bwa-0.7.17.tar.bz2 -P BWA >>log/download_BWA.log 2>&1
        tar -xf BWA/bwa-0.7.17.tar.bz2 -C BWA/ >>log/download_BWA.log 2>&1
        rm BWA/bwa-0.7.17.tar.bz2 >>log/download_BWA.log 2>&1
fi

# Download Velvet github repository
if ! [ -z "$(ls -A "velvet")" ]
then
    echo "Directory velvet/ exists and is not empty."
else
	git clone https://github.com/dzerbino/velvet.git velvet/ >>log/download_velvet.log 2>&1
	rm -rf velvet/.gitignore velvet/.git/ >>log/download_velvet.log 2>&1
fi

# Download IDBA sources
if [ -d IDBA/idba_ud-1.0.9 ]
then
	echo "Directory IDBA/idba_ud-1.0.9 already exists."
else
	wget https://s3.denbi.uni-tuebingen.de/max/idba_ud-1.0.9.tar.gz -P IDBA >>log/download_IDBA.log 2>&1
	tar -xf IDBA/idba_ud-1.0.9.tar.gz -C IDBA/ >>log/download_IDBA.log 2>&1
	rm IDBA/idba_ud-1.0.9.tar.gz >>log/download_IDBA.log 2>&1
fi

# Download GROMACS sources
if [ -d gromacs/gromacs-2018.3 ]
then
	echo "Directory gromacs/gromacs-2018.3 already exists."
else
	#wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-2018.3.tar.gz -P gromacs/
	wget https://s3.denbi.uni-tuebingen.de/max/gromacs-2018.3.tar.gz -P gromacs/ >>log/download_GROMACS.log 2>&1
	tar -xf gromacs/gromacs-2018.3.tar.gz -C gromacs/ >>log/download_GROMACS.log 2>&1
	rm gromacs/gromacs-2018.3.tar.gz >>log/download_GROMACS.log 2>&1
fi

# Download SPAdes binaries
if [ -d SPAdes/SPAdes-3.12.0-Linux ]
then
        echo "Directory SPAdes/SPAdes-3.12.0-Linux already exists."
else
	wget https://s3.denbi.uni-tuebingen.de/max/SPAdes-3.12.0-Linux.tar.gz -P SPAdes >>log/download_SPAdes.log 2>&1
	tar -xf SPAdes/SPAdes-3.12.0-Linux.tar.gz -C SPAdes >>log/download_SPAdes.log 2>&1
	rm SPAdes/SPAdes-3.12.0-Linux.tar.gz >>log/download_SPAdes.log 2>&1
fi

# Download ClustalOmega sources
if [ -d clustalOmega/clustal-omega-1.2.4 ]
then
        echo "Directory clustalOmega/clustal-omega-1.2.4 already exists."
else
        wget https://s3.denbi.uni-tuebingen.de/max/clustal-omega-1.2.4.tar.gz -P clustalOmega >>log/download_clustalOmega.log 2>&1
        tar -xf clustalOmega/clustal-omega-1.2.4.tar.gz -C clustalOmega/ >>log/download_clustalOmega.log 2>&1
        rm clustalOmega/clustal-omega-1.2.4.tar.gz >>log/download_clustalOmega.log 2>&1
fi

# Download MAFFT sources
if [ -d MAFFT/mafft-7.475-with-extensions-src ]
then
        echo "Directory MAFFT/mafft-7.475-with-extensions-src already exists."
else
        wget https://s3.denbi.uni-tuebingen.de/max/mafft-7.475-with-extensions-src.tgz -P MAFFT >>log/download_MAFFT.log 2>&1
        tar -xf MAFFT/mafft-7.475-with-extensions-src.tgz -C MAFFT/ >>log/download_MAFFT.log 2>&1
        rm MAFFT/mafft-7.475-with-extensions-src.tgz >>log/download_MAFFT.log 2>&1
fi

# Download SINA binaries
if [ -d SINA/sina-1.7.2-linux ]
then
        echo "Directory SINA/sina-1.7.2-linux already exists."
else
        wget https://s3.denbi.uni-tuebingen.de/max/sina-1.7.2-linux.tar.gz -P SINA >>log/download_SINA.log 2>&1
        tar -xf SINA/sina-1.7.2-linux.tar.gz -C SINA/ >>log/download_SINA.log 2>&1
        rm SINA/sina-1.7.2-linux.tar.gz >>log/download_SINA.log 2>&1
fi


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# Save original PATH and LD_LIBRARY variables
original_path_variable=$(echo $PATH)
original_ld_library_variable=$(echo $LD_LIBRARY_PATH)

# Compile and install GCC 7.3.0
if [ -e gcc/gcc-installed/bin/gcc ]
then 
	while true; do
        	read -p "GCC 7.3.0 seems already to be installed, do you want to recompile it?" yn
                case $yn in
                        [Yy]* ) rm -rf gcc/gcc-build/* >>log/install_gcc.log 2>&1
				rm -rf gcc/gcc-installed/* >>log/install_gcc.log 2>&1
				cd gcc/gcc-7.3.0
                                ./contrib/download_prerequisites >>../../log/install_gcc.log 2>&1
                                cd ../gcc-build
                                ../gcc-7.3.0/configure --enable-languages=c,c++ --disable-multilib --prefix=$PWD/../gcc-installed >>../../log/install_gcc.log 2>&1
                                make clean >>../../log/install_gcc.log 2>&1
                                make -j$(nproc) >>../../log/install_gcc.log 2>&1
				make install >>../../log/install_gcc.log 2>&1
                                cd ../../
                                break;;
                        [Nn]* ) echo "GCC will not be recompiled"
                                break;;
                        * ) echo "Please answer yes or no."
				;;
                esac
        done
else
        cd gcc/gcc-7.3.0
        ./contrib/download_prerequisites >>../../log/install_gcc.log 2>&1
        cd ../gcc-build
        ../gcc-7.3.0/configure --enable-languages=c,c++ --disable-multilib --prefix=$PWD/../gcc-installed >>../../log/install_gcc.log 2>&1
        make clean >>../../log/install_gcc.log 2>&1
        make -j$(nproc) >>../../log/install_gcc.log 2>&1
	make install >>../../log/install_gcc.log 2>&1
        cd ../../
fi

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# Compile and install BWA
if [ -e BWA/bwa-0.7.17/bwa ]
then
        while true; do
                read -p "BWA seems already to be installed, do you want to recompile it?" yn
                case $yn in
                        [Yy]* ) cd BWA/bwa-0.7.17/
                                make clean >>../../log/install_BWA.log 2>&1
                                make -j$(nproc) >>../../log/install_BWA.log 2>&1
                                cd ../../
                                break;;
                        [Nn]* ) echo "BWA will not be recompiled"
                                break;;
                        * ) echo "Please answer yes or no."
                                ;;
                esac
        done
else
        cd BWA/bwa-0.7.17/
        make clean >>../../log/install_BWA.log 2>&1
        make -j$(nproc) >>../../log/install_BWA.log 2>&1
        cd ../../
fi

# Compile and install bowtie2
if [ -e bowtie2/bowtie2-2.4.2/bowtie2-align-l ]
then      
        while true; do
                read -p "Bowtie2 seems already to be installed, do you want to recompile it?" yn
                case $yn in
                        [Yy]* )	cd bowtie2/bowtie2-2.4.2/
        			make clean >>../../log/install_bowtie2.log 2>&1
        			sudo make static-libs >>../../log/install_bowtie2.log 2>&1
				make -j$(nproc) STATIC_BUILD=1 >>../../log/install_bowtie2.log 2>&1
        			cd ../../
                                break;;
                        [Nn]* ) echo "Bowtie2 will not be recompiled"
                                break;;
                        * ) echo "Please answer yes or no."
                                ;;
                esac
        done
else
	cd bowtie2/bowtie2-2.4.2/
	make clean >>../../log/install_bowtie2.log 2>&1
	sudo make static-libs >>../../log/install_bowtie2.log 2>&1
	make -j$(nproc) STATIC_BUILD=1 >>../../log/install_bowtie2.log 2>&1
	cd ../../
fi

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# Set GCC to 7.3.0
export PATH=$PWD/gcc/gcc-installed/bin:$PATH
export LD_LIBRARY_PATH=$PWD/gcc/gcc-installed/lib64:$LD_LIBRARY_PATH

# Compile and install velvet
if [ -e velvet/velvetg ] && [ -e velvet/velveth ]
then
        while true; do
                read -p "Velvet seems already to be installed, do you want to recompile it?" yn
                case $yn in
                        [Yy]* ) cd velvet/
        			make clean >>../log/install_velvet.log 2>&1
        			make -j$(nproc) 'OPENMP=1' >>../log/install_velvet.log 2>&1
        			cd ..
                                break;;
                        [Nn]* ) echo "Velvet will not be recompiled"
                                break;;
                        * ) echo "Please answer yes or no."
                                ;;
                esac
        done
else
	cd velvet/
	make clean >>../log/install_velvet.log 2>&1
	make -j$(nproc) 'OPENMP=1' >>../log/install_velvet.log 2>&1
	cd ..
fi

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# Reset to system compiler as IDBA is not compiling with GCC 7.3.0
export PATH=$original_path_variable
export LD_LIBRARY_PATH=$original_ld_library_variable


# Compile and install MAFFT
if [ -e MAFFT/mafft-7.475-with-extensions/bin/mafft ]
then
        while true; do
                read -p "MAFFT seems already to be installed, do you want to recompile it?" yn
                case $yn in
                        [Yy]* ) sed -i "/PREFIX = /c\PREFIX = $PWD/MAFFT/mafft-7.475-with-extensions" MAFFT/mafft-7.475-with-extensions/core/Makefile
				cd MAFFT/mafft-7.475-with-extensions/core/
                                make clean >>../../../log/install_MAFFT.log 2>&1
                                make -j$(nproc) >>../../../log/install_MAFFT.log 2>&1
				make install >>../../../log/install_MAFFT.log 2>&1
                                cd ../../../
                                break;;
                        [Nn]* ) echo "MAFFT will not be recompiled"
                                break;;
                        * ) echo "Please answer yes or no."
                                ;;
                esac
        done
else
	sed -i "/PREFIX = /c\PREFIX = $PWD/MAFFT/mafft-7.475-with-extensions" MAFFT/mafft-7.475-with-extensions/core/Makefile
        cd MAFFT/mafft-7.475-with-extensions/core/
        make clean >>../../../log/install_MAFFT.log 2>&1
        make -j$(nproc) >>../../../log/install_MAFFT.log 2>&1
	make install >>../../../log/install_MAFFT.log 2>&1
        cd ../../../
fi

# Compile and install IDBA
if [ -e IDBA/idba_ud-1.0.9/bin/idba_ud ]
then
        while true; do
                read -p "IDBA seems already to be installed, do you want to recompile it?" yn
                case $yn in
                        [Yy]* ) cd IDBA/idba_ud-1.0.9/
				./configure >>../../log/install_IDBA.log 2>&1
				make clean >>../../log/install_IDBA.log 2>&1
				make -j$(nproc) >>../../log/install_IDBA.log 2>&1
				cd ../../
                                break;;
                        [Nn]* ) echo "IDBA will not be recompiled"
                                break;;
                        * ) echo "Please answer yes or no."
                                ;;
                esac
        done
else
	cd IDBA/idba_ud-1.0.9/
	./configure >>../../log/install_IDBA.log 2>&1
	make clean >>../../log/install_IDBA.log 2>&1
	make -j$(nproc) >>../../log/install_IDBA.log 2>&1
	cd ../../
fi

progress_bar 83 81


# Compile and install clustalOmega
if [ -e clustalOmega/clustal-omega-1.2.4/bin/clustalo ]
then
	while true; do
                read -p "clustalOmega seems already to be installed, do you want to recompile it?" yn
                case $yn in
                        [Yy]* ) cd clustalOmega/clustal-omega-1.2.4/
                                ./configure --prefix=$PWD >>../../log/install_clustalOmega.log 2>&1
                                make clean >>../../log/install_clustalOmega.log 2>&1
                                make -j$(nproc) >>../../log/install_clustalOmega.log 2>&1
				make install >>../../log/install_clustalOmega.log 2>&1
                                cd ../../
                                break;;
                        [Nn]* ) echo "ClustalOmega will not be recompiled"
                                break;;
                        * ) echo "Please answer yes or no."
                                ;;
                esac
        done
else
	cd clustalOmega/clustal-omega-1.2.4/
        ./configure --prefix=$PWD >>../../log/install_clustalOmega.log 2>&1
        make clean >>../../log/install_clustalOmega.log 2>&1
        make -j$(nproc) >>../../log/install_clustalOmega.log 2>&1
	make install >>../../log/install_clustalOmega.log 2>&1
        cd ../../
fi

progress_bar 86 83


# Compile and install tensorflow (sudo)
#check if pip is in general installed (if 0 then it is installed if 1 needs to be installed)
which pip > /dev/null 2>&1
pip_installed=$(echo $?)
if [ $pip_installed == 0 ]
then
	echo "pip is already installed, nothing to do here." >>log/install_pip.log 2>&1
else
	while true; do
                read -p "pip in general seems not to be installed or is not in your path, do you want to install it via yum?" yn
                case $yn in
                        [Yy]* ) sudo yum install pip -y >>log/install_pip.log 2>&1
                                break;;
                        [Nn]* ) echo "pip will not be installed, please install it on your own, or the Tensorflow benchmarks will not work"
                                break;;
                        * ) echo "Please answer yes or no."
                                ;;
                esac
        done
fi


#check if pip is already installed in Version 9.0.3 (if 1 then it is installed if 0 needs to be installed)
which pip > /dev/null 2>&1
pip_installed=$(echo $?)
pip_version_installed=$(pip list installed  2> /dev/null | grep -c "pip (9.0.3)")
if [ $pip_installed == 0 ] && [ $pip_version_installed == 0 ]
then
	while true; do
                read -p "pip is already installed but not in the required version 9.0.3 do you want to upgrade/downgrade to pip version 9.0.3?" yn
                case $yn in
                        [Yy]* ) sudo pip install --upgrade --force-reinstall pip==9.0.3 >>log/install_pip.log 2>&1
                                break;;
                        [Nn]* ) echo "pip will not be upgraded/downgraded to version 9.0.3, make sure tensorflow version 1.4.0 is working correctly"
                                break;;
                        * ) echo "Please answer yes or no."
                                ;;
                esac
        done
else
	echo "pip is already installed in version 9.0.3, nothing to do here." >>log/install_pip.log 2>&1
fi

#check if tensorflow is installed in version 1.4.0 (if 1 then it is installed if 0 needs to be installed)
pip_version_installed=$(pip list installed  2> /dev/null | grep -c "pip (9.0.3)")
tensorflow_installed=$(pip list installed  2> /dev/null | grep -c "tensorflow (1.4.0)")

if [ $tensorflow_installed == 0 ] && [ $pip_version_installed == 1 ]
then
	sudo pip install tensorflow==1.4.0 >>log/install_tensorflow.log 2>&1
elif [ $tensorflow_installed == 1 ] && [ $pip_version_installed == 1 ]
then 
	while true; do
                read -p "Tensorflow seems already to be installed in version 1.4.0 via pip, do you want to reinstall it?" yn
                case $yn in
                        [Yy]* ) sudo pip install --force-reinstall tensorflow==1.4.0 >>log/install_tensorflow.log 2>&1
                                break;;
                        [Nn]* ) echo "Tensorflow will not be reinstalled"
                                break;;
                        * ) echo "Please answer yes or no."
                                ;;
                esac
        done
else 
	echo "Something seems to be wrong with the pip and tensorflow installation please check if pip is installed in version 9.0.3 and tensorflow in version 1.4.0."
fi


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# Set GCC to 7.3.0 to fasten up GROMACS
export PATH=$PWD/gcc/gcc-installed/bin:$PATH
export LD_LIBRARY_PATH=$PWD/gcc/gcc-installed/lib64:$LD_LIBRARY_PATH

# Compile and install GROMACS (sudo)
if [ -e /usr/local/gromacs/bin/gmx ]
then
        while true; do
                read -p "GROMACS seems already to be installed, do you want to recompile it?" yn
                case $yn in
                        [Yy]* ) rm -rf gromacs/gromacs-2018.3/build/* >>log/install_GROMACS.log 2>&1
				sudo rm -rf /usr/local/gromacs/ >>log/install_GROMACS.log 2>&1
				cd gromacs/gromacs-2018.3/build/
				CC=gcc CXX=g++ cmake3 -DCMAKE_CXX_COMPILER=g++ -DGMX_BUILD_OWN_FFTW=on -DGMX_GPU=off -DGMX_BUILD_MPI=off --build ./ ../../gromacs-2018.3/ >>../../../log/install_GROMACS.log 2>&1
				make clean >>../../../log/install_GROMACS.log 2>&1
				make -j$(nproc) >>../../../log/install_GROMACS.log 2>&1
				sudo make install >>../../../log/install_GROMACS.log 2>&1
				cd ../../../
				break;;
                        [Nn]* ) echo "GROMACS will not be recompiled"
                                break;;
                        * ) echo "Please answer yes or no."
                                ;;
                esac
        done
else
	mkdir gromacs/gromacs-2018.3/build
	cd gromacs/gromacs-2018.3/build/
	CC=gcc CXX=g++ cmake3 -DCMAKE_CXX_COMPILER=g++ -DGMX_BUILD_OWN_FFTW=on -DGMX_GPU=off -DGMX_BUILD_MPI=off --build ./ ../../gromacs-2018.3/ >>../../../log/install_GROMACS.log 2>&1
	make clean >>../../../log/install_GROMACS.log 2>&1
	make -j	$(nproc) >>../../../log/install_GROMACS.log 2>&1
	sudo make install >>../../../log/install_GROMACS.log 2>&1
	cd ../../../
	#/usr/local/gromacs/bin/gmx grompp -f datasets/gromacs/adh_cubic/pme_verlet.mdp -c datasets/gromacs/adh_cubic/conf.gro -p datasets/gromacs/adh_cubic/topol.top -o datasets/gromacs/adh_cubic/topol -po datasets/gromacs/adh_cubic/mdout
fi

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# Convert fastq files to fasta files
echo "Converting datasets from .fastq to .fa" >>log/file_conversion_ERR016155.log 2>&1

if [ -e datasets/1000_genomes/ERR016155.filt.fa ]
then
	echo "File datasets/1000_genomes/ERR016155.filt.fa already exists."
else
	IDBA/idba_ud-1.0.9/bin/fq2fa datasets/1000_genomes/ERR016155.filt.fastq datasets/1000_genomes/ERR016155.filt.fa >>log/file_conversion_ERR016155.log 2>&1
fi

if [ -e datasets/1000_genomes/ERR251006.filt.fa ]
then
        echo "File datasets/1000_genomes/ERR251006.filt.fa already exists."
else
	IDBA/idba_ud-1.0.9/bin/fq2fa datasets/1000_genomes/ERR251006.filt.fastq datasets/1000_genomes/ERR251006.filt.fa >>log/file_conversion_ERR251006.log 2>&1
fi

if [ -e datasets/1000_genomes/ERR015528.filt.fa ]
then
        echo "File datasets/1000_genomes/ERR015528.filt.fa already exists."
else
        IDBA/idba_ud-1.0.9/bin/fq2fa datasets/1000_genomes/ERR015528.filt.fastq datasets/1000_genomes/ERR015528.filt.fa >>log/file_conversion_ERR015528.log 2>&1
fi

if [ -e datasets/1000_genomes/SRR741411.filt.fa ]
then
        echo "File datasets/1000_genomes/SRR741411.filt.fa already exists."
else
        IDBA/idba_ud-1.0.9/bin/fq2fa datasets/1000_genomes/SRR741411.filt.fastq datasets/1000_genomes/SRR741411.filt.fa >>log/file_conversion_SRR741411.log 2>&1
fi

if [ -e datasets/ebi/DRR001012.fa ]
then
        echo "File datasets/ebi/DRR001012.fa already exists."
else
	IDBA/idba_ud-1.0.9/bin/fq2fa datasets/ebi/DRR001012.fastq datasets/ebi/DRR001012.fa >>log/file_conversion_DRR001012.log 2>&1
fi

if [ -e datasets/ebi/DRR001025.fa ]
then
        echo "File datasets/ebi/DRR001025.fa already exists."
else
	IDBA/idba_ud-1.0.9/bin/fq2fa datasets/ebi/DRR001025.fastq datasets/ebi/DRR001025.fa >>log/file_conversion_DRR001025.log 2>&1
fi

if [ -e datasets/SINA/OE-38_R1.fa ]
then
        echo "File datasets/SINA/OE-38_R1.fa already exists."
else
        IDBA/idba_ud-1.0.9/bin/fq2fa datasets/SINA/OE-38_R1.fastq datasets/SINA/OE-38_R1.fa >>log/file_conversion_DRR001025.log 2>&1
fi


# Reset to system compiler after finishing installation process
export PATH=$original_path_variable
export LD_LIBRARY_PATH=$original_ld_library_variable

progress_bar 100 95
echo "BOOTABLE should be successfully installed, please check with the install_check.sh tool."