setup_conda.sh

#!/bin/bash

sys="$(uname)" # Linux for Linux or Darwin for MacOS
echo "Current OS system: $sys"

flag=0
### check grep, sed and wget availability
echo "-------------------------------------"
echo "Checking .bash_profile/.bashrc, grep, sed/gsed and wget availability..."
grepprog='grep'
sedprog='sed'
wgetprog='wget'
bashFile='.bashrc'
rprofile='.Rprofile'

if [ "$sys" == "Darwin" ]; then
    sedprog='gsed'
	grepprog='ggrep'
	shell=$(echo $SHELL)
	if [ $shell == "/bin/zsh" ]; then
    	bashFile='.zshrc'
	else
		bashFile='.bash_profile'
	fi
fi

# NOTE: install only available for Linux!
if [ -z "$(which $sedprog)" ]; then
    if [ "$sys" == "Darwin" ]; then
        echo -e "\e[31m$sedprog not found. Please install it first (e.g. using brew)!\e[0m"
        flag=1
    fi
	conda install -c conda-forge sed
fi

if [ -z "$(which $grepprog)" ]; then
    if [ "$sys" == "Darwin" ]; then
        echo -e "\e[31m$grepprog not found. Please install it first (e.g. using brew)!\e[0m"
        flag=1
    fi
	conda install -c bioconda grep
fi

if [ -z "$(which $wgetprog)" ]; then
    if [ "$sys" == "Darwin" ]; then
        echo -e "\e[31m$wgetprog not found. Please install it first (e.g. using brew)!\e[0m"
        flag=1
    fi
	conda install -c anaconda wget
fi

if ! [ -f ~/$bashFile ]; then
    touch ~/$bashFile
fi
if ! [ -f ~/$rprofile ]; then
    touch ~/$rprofile
fi
if [ "$flag" == 1 ]; then exit 1; fi
echo "done!"

### check dependencies
echo "-------------------------------------"
echo "Installing dependencies..."

if [ -z "$(which R)" ]; then
    echo "R"
    conda install -y r
fi

if [[ -z $(conda list | $grepprog "pkg-config ") ]]; then
    echo "pkg-config"
    conda install -y pkg-config
fi

if [[ -z $(conda list | $grepprog "perl-bioperl ") ]]; then
    echo "perl-bioperl"
    conda install -y -c bioconda perl-bioperl
    conda install -y -c bioconda perl-bioperl-core
    conda install -y -c bioconda perl-bioperl-run
fi

dependencies=(
  blastp # blast
  genewise # wise2
  hmmsearch # hmmer (for both hmmsearch and hmmbuild)
  clustalw
  mafft # for linsi
  muscle
  fasta36
)

for i in "${dependencies[@]}"; do
  if [ -z "$(which $i)" ]; then
    echo $i
    tool=$i
    if [ "$tool" = "blastp" ]; then
      conda install -y -c bioconda blast
    elif [ "$tool" = "hmmsearch" ]; then
      conda install -y -c bioconda hmmer
    elif [ "$tool" = "genewise" ]; then
      conda install -y -c bioconda wise2
      wisePath=$(which "genewise")
      if [ -z "$($grepprog WISECONFIGDIR=$wisePath ~/$bashFile)" ]; then
          echo "export WISECONFIGDIR=${wisePath}" >> ~/$bashFile
      fi
    elif [ "$tool" = "fasta36" ]; then
        conda install -y -c bioconda fasta3
    else
      conda install -y -c bioconda $i
    fi
  fi
done

for i in "${dependencies[@]}"; do
  if [ -z "$(which $i)" ]; then
    echo -e "\e[31m$i not found. Please install it to use HaMStR!\e[0m"
    flag=1
  fi
done
if [ "$flag" == 1 ]; then exit 1; fi

perlModules=(
  Capture::Tiny
  DBI
  DB_File
  File::Copy
  File::Path
  File::Basename
  File::Which
  List::Util
  Parallel::ForkManager
  POSIX
  XML::SAX
  XML::NamespaceSupport
  XML::Parser
  Getopt::Long
  IO::Handle
  IPC::Run
  Statistics::R
  Term::Cap
  Time::HiRes
  Bio::AlignIO
  Bio::Align::ProteinStatistics
  Bio::DB::Taxonomy
  Bio::SearchIO
  Bio::SearchIO::blastxml
  Bio::Search::Hit::BlastHit
  Bio::Seq
  Bio::SeqIO
  Bio::SeqUtils
  Bio::Tree::Tree
  Bio::Tools::Run::StandAloneBlast
)

for i in "${perlModules[@]}"; do
  msg=$((perldoc -l $i) 2>&1)
  if [[ "$(echo $msg)" == *"No documentation"* ]]; then
    cpanm ${i} --quiet --force
  fi
done

echo "done!"

### prepare folders
echo "-------------------------------------"
echo "Preparing folders..."
CURRENT="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"

# create required folders
folders=(
  blast_dir
  core_orthologs
  genome_dir
  weight_dir
  taxonomy
  output
  tmp
)

for i in "${folders[@]}"; do
    if [ ! -d "$CURRENT/$i" ]; then mkdir "$CURRENT/$i"; fi
done
echo "done!"

### download tools
echo "-------------------------------------"
echo "Downloading and installing annotation tools/databases:"

cd "taxonomy"
if ! [ -f "nodes" ]; then
  wget "ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz"
  tar xfv taxdump.tar.gz
  rm taxdump.tar.gz
  echo "Taxonomy database indexing. It can take a while, please wait..."
  perl $CURRENT/bin/indexTaxonomy.pl $CURRENT/taxonomy
  rm citations.dmp
  rm delnodes.dmp
  rm division.dmp
  rm gencode.dmp
  rm merged.dmp
  rm gc.prt
  rm readme.txt
fi
cd $CURRENT
if ! [ -f "$CURRENT/taxonomy/nodes" ]; then
	echo -e "\e[31mError while indexing NCBI taxonomy database! Please check $CURRENT/taxonomy/ folder and run this setup again!\e[0m"
	exit
fi

cd "bin"
fasPrepare=0
if [ -z "$(which greedyFAS)" ]; then
    echo "FAS"
    conda install -y -c BIONF fas
    if [ -z "$(which annoFAS)" ]; then
        echo -e "\e[31mInstallation of FAS failed! Please try again!\e[0m"
        exit
    fi
    fasPrepare=1
else
    fasPath="$(pip show greedyFAS | $grepprog Location | $sedprog 's/Location: //')"
    annoFile="$fasPath/greedyFAS/annoFAS.pl"
    tmp="$($grepprog "my \$config" $annoFile | $sedprog 's/my \$config = //' | $sedprog 's/;//')"
    if [ $tmp == "1" ]; then
        annoPath="$($grepprog "my \$annotationPath" $annoFile | $sedprog 's/my \$annotationPath = "//' | $sedprog 's/";//')"
        if ! [ -f "$annoPath/Pfam/Pfam-hmms/Pfam-A.hmm" ]; then
            fasPrepare=1
        fi
    else
        fasPrepare=1
    fi
fi

if [ -z "$(which annoFAS)" ]; then
    echo -e "Installation of FAS failed! Please try again or install FAS by yourself using \e[91mconda install -c BIONF fas\e[0m"
    echo -e "For more info, please check FAS website at \e[91mhttps://github.com/BIONF/FAS\e[0m"
    exit
else
    fasPath="$(pip show greedyFAS | $grepprog Location | $sedprog 's/Location: //')"
    annoFile="$fasPath/greedyFAS/annoFAS.pl"
    tmp="$($grepprog "my \$config" $annoFile | $sedprog 's/my \$config = //' | $sedprog 's/;//')"
    if [ $tmp == "0" ]; then
        fasPrepare=1
    fi
fi
cd $CURRENT
echo "done!"

### download data
echo "-------------------------------------"
echo "Getting pre-calculated data"

data_HaMStR_file="data_HaMStR-2019.tar.gz"
checkSumData="1303809705 685885017 $data_HaMStR_file"

if ! [ "$(ls -A $CURRENT/genome_dir)" ]; then
	echo "Processing $CURRENT ..."
	if [ ! -f $CURRENT/$data_HaMStR_file ]; then
		echo "Downloading data from https://applbio.biologie.uni-frankfurt.de/download/hamstr_qfo/$data_HaMStR_file"
		wget --no-check-certificate https://applbio.biologie.uni-frankfurt.de/download/hamstr_qfo/$data_HaMStR_file
	else
		CHECKSUM=$(cksum $data_HaMStR_file)
		echo "Checksum: $CHECKSUM"
		if ! [ "$CHECKSUM" == "$checkSumData" ]; then
    		  rm $CURRENT/$data_HaMStR_file
    		  echo "Downloading data from https://applbio.biologie.uni-frankfurt.de/download/hamstr_qfo/$data_HaMStR_file"
      		  wget --no-check-certificate https://applbio.biologie.uni-frankfurt.de/download/hamstr_qfo/$data_HaMStR_file
    	fi
    fi

	if [ ! -f $CURRENT/$data_HaMStR_file ]; then
	  echo "File $data_HaMStR_file not found! Please try to download again from"
	  echo "https://applbio.biologie.uni-frankfurt.de/download/hamstr_qfo/data_HaMStR.tar"
	  exit
	fi

	CHECKSUM=$(cksum $data_HaMStR_file)
	if [ "$CHECKSUM" == "$checkSumData" ]; then
	  echo "Extracting archive $data_HaMStR_file..."
	  tar xf $CURRENT/$data_HaMStR_file
	  rm $CURRENT/$data_HaMStR_file
    for i in $(ls "$CURRENT/genome_dir"); do rm "$CURRENT/genome_dir/$i/$i.fa.mod"; done

    if [ "$(ls -A $CURRENT/blast_dir)" ]; then
        echo "Data should be in place to run HaMStR.\n"
    else
        echo -e "\e[31mSomething went wrong with the download. Data folders are empty.\e[0m"
      echo "Please try to download again from"
      echo "https://applbio.biologie.uni-frankfurt.de/download/hamstr_qfo/$data_HaMStR_file"
      echo "Or contact us if you think this is our issue!"
      exit
    fi
	else
	  echo -e "\e[31mSomething went wrong with the download. Checksum does not match.\e[0m"
	  echo "Please try to download again from"
	  echo "https://applbio.biologie.uni-frankfurt.de/download/hamstr_qfo/$data_HaMStR_file"
	  echo "Please put it into $CURRENT folder and run this setup again!"
	  exit
	fi
fi

### add paths to bash profile file
echo "-------------------------------------"
echo "Adding paths to ~/$bashFile"

if [ -z "$($grepprog PATH=$CURRENT/bin:\$PATH ~/$bashFile)" ]; then
	echo "export PATH=$CURRENT/bin:\$PATH" >> ~/$bashFile
fi

wisePath=$(which "genewise")
if [ -z "$($grepprog WISECONFIGDIR=$wisePath ~/$bashFile)" ]; then
    echo "export WISECONFIGDIR=${wisePath}" >> ~/$bashFile
fi

echo "Adding paths to ~/$rprofile"
if [ -z "$($grepprog $CURRENT/bin ~/$rprofile)" ]; then
    echo "Sys.setenv(PATH = paste(\"$CURRENT/bin\", Sys.getenv(\"PATH\"), sep=\":\"))" >> ~/$rprofile
fi

echo "done!"

### adapt paths in hamstr scripts
echo "-------------------------------------"
echo "Adapting paths in hamstr scripts"
# update the sed and grep commands
$sedprog -i -e "s/\(my \$sedprog = '\).*/\1$sedprog';/" $CURRENT/bin/hamstr.pl
$sedprog -i -e "s/\(my \$grepprog = '\).*/\1$grepprog';/" $CURRENT/bin/hamstr.pl
$sedprog -i -e "s/\(my \$sedprog = '\).*/\1$sedprog';/" $CURRENT/bin/oneSeq.pl
$sedprog -i -e "s/\(my \$grepprog = '\).*/\1$grepprog';/" $CURRENT/bin/oneSeq.pl

# localize the perl installation
path2perl=`which perl`
echo "path to perl: $path2perl"
$sedprog -i -e "s|\#\!.*|\#\!$path2perl|g" $CURRENT/bin/hamstr.pl
$sedprog -i -e "s|\#\!.*|\#\!$path2perl|g" $CURRENT/bin/nentferner.pl
$sedprog -i -e "s|\#\!.*|\#\!$path2perl|g" $CURRENT/bin/translate.pl
$sedprog -i -e "s|\#\!.*|\#\!$path2perl|g" $CURRENT/bin/oneSeq.pl

### final check
echo "-------------------------------------"
echo "Final check..."
flag=0

echo "Conda packages"
condaPkgs=(
  perl-bioperl
  perl-bioperl-core
  blast
  hmmer
  wise2
  clustalw
  mafft
  muscle
  fasta3
)
for i in "${condaPkgs[@]}"; do
    if [[ -z $(conda list | $grepprog "$i ") ]]; then
        progname=$i
        if [ "$i" == "blast" ]; then
            progname="blastp"
        elif [ "$i" == "wise2" ]; then
            progname="genewise"
        elif [ "$i" == "hmmer" ]; then
            progname="hmmsearch"
        elif [ "$i" == "fasta3" ]; then
            progname="fasta36"
        fi
        if [ -z "$(which $progname)" ]; then
            echo -e "\t\e[31m$i could not be installed\e[0m"
            flag=1
        fi
    fi
done
echo "done!"

echo "Perl modules"
for i in "${perlModules[@]}"; do
  msg=$((perl -e "use $i") 2>&1)
  if ! [[ -z ${msg} ]]; then
    echo -e "\t\e[31m$i could not be installed\e[0m"
    flag=1
  fi
done
echo "done!"

echo "Environment paths"
envPaths=(
  WISECONFIGDIR
)
for i in "${envPaths[@]}"; do
    if [ -z "$($grepprog $i ~/$bashFile)" ]; then
        echo -e "\t\e[31m$i was not added into ~/$bashFile\e[0m"
        flag=1
    fi
done

if [ -z "$($grepprog PATH=$CURRENT/bin:\$PATH ~/$bashFile)" ]; then
	echo -e "\t\e[31m$CURRENT/bin was not added into ~/$bashFile\e[0m"
fi
if [ -z "$($grepprog $CURRENT/bin ~/$rprofile)" ]; then
	echo -e "\t\e[31mWARNING $CURRENT/bin was not added into ~/$rprofile\e[0m"
    flag=1
fi

echo "done!"

if [ "$flag" == 1 ]; then
    echo "Some tools were not installed correctly or paths were not added into ~/$bashFile or ~/$rprofile."
    echo "Please install the missing dependencies using $CURRENT/install_lib.sh script (or ask your admin if you don't have root privileges)."
    echo "Then run this setup again to try one more time!"
    exit
else
    echo "Generating symbolic links"
    ln -s -f $CURRENT/bin/hamstr.pl $CURRENT/bin/hamstr
    ln -s -f $CURRENT/bin/oneSeq.pl $CURRENT/bin/oneSeq
    echo "Sourcing bash profile file"
    source ~/$bashFile
    echo "-------------------------------------"
    $sedprog -i -e 's/my $configure = .*/my $configure = 1;/' $CURRENT/bin/hamstr.pl
    $sedprog -i -e 's/my $configure = .*/my $configure = 1;/' $CURRENT/bin/oneSeq.pl
    if [ "$fasPrepare" == 1 ]; then
        echo "All tests succeeded."
        echo -e "\e[91mPLEASE RUN\e[0m \e[96mprepareFAS\e[0m \e[91mTO CONFIGURE FAS BEFORE USING HaMStR!\e[0m"
        echo "Then you can test HaMStR with:"
    else
        echo "All tests succeeded, HaMStR should be ready to run. You can test it with:"
    fi
    echo -e "\e[96mcd HaMStR\e[0m"
    echo -e "\e[96moneSeq -seqFile=infile.fa -seqName=test -refspec=HUMAN@9606@3 -minDist=genus -maxDist=kingdom -coreOrth=5 -cleanup -cpu=4\e[0m"
    echo "Output files with prefix \"test\" will be found at your current working directory!"
    echo -e "For more details, use \e[96moneSeq -h\e[0m"
    echo -e "\e[91mNote: if oneSeq not found, you should run this command first:\e[0m \e[96msource ~/$bashFile\e[0m"
    echo "Happy HaMStRing! ;-)"
fi
exit 1