INSTALL.sh

#!/usr/bin/env bash

set -e # Exit as soon as any line in the bash script fails

ROOTDIR=$( cd $(dirname $0) ; pwd -P ) # path to main PhaME directory

echo
exec &> >(tee -a  install.log)
exec 2>&1 # copies stderr onto stdout

# create a directory where all dependencies will be installed
cd $ROOTDIR
mkdir -p thirdParty
cd thirdParty
mkdir -p $ROOTDIR/bin
export PATH="$ROOTDIR/bin/":"$ROOTDIR/thirdParty/miniconda/bin/":$PATH
# Minimum Required versions of dependencies
# nucmer 3.1 is packaged in mummer 3.23
bowtie2_VER=2.3.0
bwa_VER=0.7.15
cmake_VER=3.0.1
cpanm_VER=1.7039
FastTree_VER=2.1.9
mafft_VER=7.305
miniconda_VER=4.4.11
mummer_VER=3.23
muscle_VER=3.8.31
paml_VER=4.9
R_VER=3.3.1
RAxML_VER=8.2.10
samtools_VER=1.3.1
perl5_VER=5.26.2
bcftools_VER=1.6
hyphy_VER=2.3.11
bbmap_VER=37.62

#minimum required version of Perl modules
perl_File_Basename_VER=2.85
perl_File_Path_VER=2.09
perl_Getopt_Long_VER=2.45
perl_IO_Handle_VER=1.28
perl_Parllel_ForkManager_VER=1.17
# perl_Time_BaseName=2.85
perl_Time_HiRes=1.9726
perl_Statistics_Distributions_VER=1.02
perl_Test_Exception_VER=0.43
perl_Time_HiRes_VER=1.9758
perl_File_Copy_VER=2.21 


################################################################################
done_message () {
   if [ $? == 0 ]; then
      if [ "x$1" != "x" ]; then
          echo $1;
      else
          echo "done.";
      fi
   else
      echo "Installation failed." $2
      exit 1;
   fi
}

################################################################################
install_miniconda()
{
echo "--------------------------------------------------------------------------
                           downloading miniconda
--------------------------------------------------------------------------------
"

if [[ "$OSTYPE" == "darwin"* ]]
then
{

    curl -o miniconda.sh https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
    chmod +x miniconda.sh
    ./miniconda.sh -b -p $ROOTDIR/thirdParty/miniconda -f
    conda update --yes -n base conda
    ln -sf $ROOTDIR/thirdParty/miniconda/bin/conda $ROOTDIR/bin/conda
    ln -sf $ROOTDIR/thirdParty/miniconda/bin/pip $ROOTDIR/bin/pip
}
else
{  

    wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
    chmod +x miniconda.sh
    ./miniconda.sh -b -p $ROOTDIR/thirdParty/miniconda -f
    conda update --yes -n base conda
    ln -sf $ROOTDIR/thirdParty/miniconda/bin/conda $ROOTDIR/bin/conda
    ln -sf $ROOTDIR/thirdParty/miniconda/bin/pip $ROOTDIR/bin/pip

}
fi
}

################################################################################
checkSystemInstallation()
{
    IFS=:
    for d in $PATH; do
      if test -x "$d/$1"; then return 0; fi
    done
    return 1
}


checkLocalInstallation()
{
    IFS=:
    for d in $ROOTDIR/thirdParty/miniconda/bin; do
      if test -x "$d/$1"; then return 0; fi
    done
    return 1
}

checkHyPhyInstallation()
{
    IFS=:
    for d in $ROOTDIR/bin; do
      if test -x "$d/$1"; then return 0; fi
    done
    return 1
}

checkPerlModule()
{
   perl -e "use lib \"$ROOTDIR/lib\"; use $1;"
   return $?
}

# ################################################################################
# install_cpan()
# {
# echo "--------------------------------------------------------------------------
#                            installing cpanm v2.00
# --------------------------------------------------------------------------------
# "
# conda install --yes c dan_blanchard perl-cpan=2.00 -p $ROOTDIR/thirdParty/miniconda
# ln -sf $ROOTDIR/thirdParty/miniconda/bin/cpan $ROOTDIR/bin/cpan
# echo "--------------------------------------------------------------------------
#                            installed cpanm v2.00
# --------------------------------------------------------------------------------
# "

# }

# ################################################################################
# install_cpanm()
# {
# echo "--------------------------------------------------------------------------
#                            installing cpanm v1.7039 
# --------------------------------------------------------------------------------
# "
# conda install --yes -c bioconda perl-app-cpanminus=$cpanm_VER -p $ROOTDIR/thirdParty/miniconda
# ln -sf $ROOTDIR/thirdParty/miniconda/bin/cpanm $ROOTDIR/bin/cpanm
# echo "--------------------------------------------------------------------------
#                           cpanm v1.7039 installed
# --------------------------------------------------------------------------------
# "
# }

# install_mummer()
# {
# echo "--------------------------------------------------------------------------
#                            installing mummer v3.23 or nucmer 3.21
# --------------------------------------------------------------------------------
# "
# conda install --yes -c bioconda mummer=$mummer_VER -p $ROOTDIR/thirdParty/miniconda
# ln -sf $ROOTDIR/thirdParty/miniconda/opt/mummer-$mummer_VER/nucmer $ROOTDIR/bin/nucmer
# ln -sf $ROOTDIR/thirdParty/miniconda/bin/mummer $ROOTDIR/bin/mummer
# ln -sf $ROOTDIR/thirdParty/miniconda/bin/delta-filter $ROOTDIR/bin/delta-filter
# ln -sf $ROOTDIR/thirdParty/miniconda/bin/show-snps $ROOTDIR/bin/show-snps
# ln -sf $ROOTDIR/thirdParty/miniconda/bin/show-coords $ROOTDIR/bin/show-coords
# # conda install --yes -c bioconda mummer=$mummer_VER -p $ROOTDIR/thirdParty/miniconda
# echo "
# ------------------------------------------------------------------------------
#                            mummer v3.23 installed or nucmer 3.21
# ------------------------------------------------------------------------------
# "
# }
# install_bbmap()
# {
# echo "--------------------------------------------------------------------------
#                            installing bbmap v37.62
# --------------------------------------------------------------------------------
# "
# conda install --yes -c bioconda bbmap -p $ROOTDIR/thirdParty/miniconda
# ln -sf $ROOTDIR/thirdParty/miniconda/bin/bbmap.sh $ROOTDIR/bin/bbmap.sh
# ln -sf $ROOTDIR/thirdParty/miniconda/bin/sketch.sh $ROOTDIR/bin/sketch.sh
# ln -sf $ROOTDIR/thirdParty/miniconda/bin/comparesketch.sh $ROOTDIR/bin/comparesketch.sh

# echo "
# ------------------------------------------------------------------------------
#                            mummer v37.62 
# ------------------------------------------------------------------------------
# "
# }


# install_cmake()
# {
# echo "--------------------------------------------------------------------------
#                            installing cmake v3.0.1
# --------------------------------------------------------------------------------
# "
# conda install --yes -c anaconda cmake=$cmake_VER -p $ROOTDIR/thirdParty/miniconda
# ln -sf $ROOTDIR/thirdParty/miniconda/bin/cmake $ROOTDIR/bin/cmake
# echo "
# ------------------------------------------------------------------------------
#                            cmake v3.0.1 installed
# ------------------------------------------------------------------------------
# "
# }

# install_bwa()
# {
# echo "------------------------------------------------------------------------------
#                            Downloading bwa v0.7.15
# ------------------------------------------------------------------------------
# "
# conda install --yes -c bioconda bwa=$bwa_VER -p $ROOTDIR/thirdParty/miniconda
# ln -sf $ROOTDIR/thirdParty/miniconda/bin/bwa $ROOTDIR/bin/bwa
# echo "
# ------------------------------------------------------------------------------
#                            bwa v0.7.15 installed
# ------------------------------------------------------------------------------
# "
# }

# install_bowtie2()
# {
# echo "--------------------------------------------------------------------------
#                            installing bowtie2 v2.3.0
# --------------------------------------------------------------------------------
# "
# conda install --yes -c bioconda bowtie2=$bowtie2_VER -p $ROOTDIR/thirdParty/miniconda
# ln -sf $ROOTDIR/thirdParty/miniconda/bin/bowtie2 $ROOTDIR/bin/bowtie2
# echo "
# ------------------------------------------------------------------------------
#                            bowtie2 v2.3.0 installed
# ------------------------------------------------------------------------------
# "
# }

# install_samtools()
# {
# echo "--------------------------------------------------------------------------
#                            Downloading samtools v1.3.1
# --------------------------------------------------------------------------------
# "
# conda install --yes -c bioconda samtools=$samtools_VER -p $ROOTDIR/thirdParty/miniconda
# ln -sf $ROOTDIR/thirdParty/miniconda/bin/samtools $ROOTDIR/bin/samtools
# echo "
# --------------------------------------------------------------------------------
#                            samtools v1.3.1 installed
# --------------------------------------------------------------------------------
# "
# }

# install_FastTree()
# {
# echo "--------------------------------------------------------------------------
#                            Downloading FastTree v2.1.9
# --------------------------------------------------------------------------------
# "
# conda install --yes -c bioconda FastTree=$FastTree_VER -p $ROOTDIR/thirdParty/miniconda
# ln -sf $ROOTDIR/thirdParty/miniconda/bin/FastTree $ROOTDIR/bin/FastTree
# ln -sf $ROOTDIR/thirdParty/miniconda/bin/FastTreeMP $ROOTDIR/bin/FastTreeMP
# echo "
# --------------------------------------------------------------------------------
#                            FastTree v2.1.9
# --------------------------------------------------------------------------------
# "
# }

# install_RAxML()
# {
# echo "--------------------------------------------------------------------------
#                            Downloading RAxML v$RAxML_VER
# --------------------------------------------------------------------------------
# "
# conda install --yes -c bioconda RAxML=$RAxML_VER -p $ROOTDIR/thirdParty/miniconda
# ln -sf $ROOTDIR/thirdParty/miniconda/bin/raxmlHPC $ROOTDIR/bin/raxmlHPC
# ln -sf $ROOTDIR/thirdParty/miniconda/bin/raxmlHPC $ROOTDIR/bin/raxmlHPC-PTHREADS
# echo "
# --------------------------------------------------------------------------------
#                            RAxML v$RAxML_VER
# --------------------------------------------------------------------------------
# "
# }

# install_muscle()
# {
# echo "--------------------------------------------------------------------------
#                            Downloading muscle v3.8.31
# --------------------------------------------------------------------------------
# "
# conda install --yes -c bioconda muscle=$muscle_VER -p $ROOTDIR/thirdParty/miniconda
# ln -sf $ROOTDIR/thirdParty/miniconda/bin/muscle $ROOTDIR/bin/muscle
# echo "
# --------------------------------------------------------------------------------
#                            muscle v3.8.31
# --------------------------------------------------------------------------------
# "
# }

# install_mafft()
# {
# echo "--------------------------------------------------------------------------
#                            Downloading mafft v7.305
# --------------------------------------------------------------------------------
# "
# conda install --yes -c bioconda mafft=$mafft_VER -p $ROOTDIR/thirdParty/miniconda
# ln -sf $ROOTDIR/thirdParty/miniconda/bin/mafft $ROOTDIR/bin/mafft
# echo "
# --------------------------------------------------------------------------------
#                            mafft v7.305
# --------------------------------------------------------------------------------
# "
# }

# install_paml()
# {
# echo "--------------------------------------------------------------------------
#                            Downloading paml v4.9
# --------------------------------------------------------------------------------
# "
# conda install --yes -c bioconda paml=$paml_VER -p $ROOTDIR/thirdParty/miniconda
# echo "
# --------------------------------------------------------------------------------
#                            paml v4.9
# --------------------------------------------------------------------------------
# "
# }

# install_bcftools()
# {
# echo "--------------------------------------------------------------------------
#                            installing bcftools v$bcftools_VER
# --------------------------------------------------------------------------------
# "
# conda install --yes -c bioconda bcftools=$bcftools_VER -p $ROOTDIR/thirdParty/miniconda
# ln -sf $ROOTDIR/thirdParty/miniconda/bin/bcftools $ROOTDIR/bin/bcftools
# echo "--------------------------------------------------------------------------
#                            installed bcftools v$bcftools_VER
# --------------------------------------------------------------------------------
# "
# }

install_hyphy()
{
echo "--------------------------------------------------------------------------
                           installing hyphy v$hyphy_VER
--------------------------------------------------------------------------------
"
#curl -o thirdParty/hyphy-2.3.11.zip https://github.com/veg/hyphy/archive/2.3.11.zip
cd $ROOTDIR
unzip thirdParty/hyphy-2.3.11.zip -d thirdParty/;
gcc -v;
which gcc;
cd $ROOTDIR/thirdParty/hyphy-2.3.11;
cmake -DINSTALL_PREFIX=$ROOTDIR/thirdParty/hyphy-2.3.11
make MP
make install
make GTEST
cd $ROOTDIR
ln -sf $ROOTDIR/thirdParty/hyphy-2.3.11/HYPHYMP $ROOTDIR/bin/HYPHYMP
echo "--------------------------------------------------------------------------
                           installed hyphy v$hyphy_VER
--------------------------------------------------------------------------------
"
}

# install_perl_Getopt_Long()
# {
# echo "--------------------------------------------------------------------------
#                 installing Perl Module Getopt::Long v2.45
# --------------------------------------------------------------------------------
# "
# cpanm Getopt::Long@$perl_Getopt_Long_VER
# echo "
# --------------------------------------------------------------------------------
#                            Getopt::Long v2.45 installed
# --------------------------------------------------------------------------------
# "
# }
# install_perl_Test_Exception()
# {
# echo "--------------------------------------------------------------------------
#                 installing Perl Module Test::Exception v0.46
# --------------------------------------------------------------------------------
# "
# cpanm Test::Exception@$perl_Test_Exception_VER
# echo "
# --------------------------------------------------------------------------------
#                            Test::Exception v0.46 installed
# --------------------------------------------------------------------------------
# "
# }

# install_perl_Statistics_Distributions()
# {
# echo "--------------------------------------------------------------------------
#           installing Perl Module Statistics::Distributions v1.02
# --------------------------------------------------------------------------------
# "
# cpanm Statistics::Distributions@$perl_Statistics_Distributions_VER
# echo "
# --------------------------------------------------------------------------------
#                           Statistics::Distributions v1.02 installed
# --------------------------------------------------------------------------------
# "
# }

# install_perl_Time_HiRes()
# {
# echo "--------------------------------------------------------------------------
#                            installing Perl Module Time::HiRes v1.9726
# --------------------------------------------------------------------------------
# "
# cpanm Time::HiRes@$perl_Time_HiRes_VER
# echo "
# --------------------------------------------------------------------------------
#                           Time::HiRes v1.9726 installed
# --------------------------------------------------------------------------------
# "
# }

# install_perl_File_Path()
# {
# echo "--------------------------------------------------------------------------
#                            installing Perl Module File::Path v2.09
# --------------------------------------------------------------------------------
# "
# cpanm File::Path@$perl_File_Path_VER
# echo "
# --------------------------------------------------------------------------------
#                           File::Path v2.09 installed 
# --------------------------------------------------------------------------------
# "
# }

# install_perl_File_Basename()
# {
# echo "--------------------------------------------------------------------------
#                            installing Perl Module File::Basename v2.85
# --------------------------------------------------------------------------------
# "
# cpanm File::Basename@$perl_File_Basename_VER
# echo "
# --------------------------------------------------------------------------------
#                           File::Basename Resinstalled v2.85
# --------------------------------------------------------------------------------
# "
# }

# install_perl_File_Copy()
# {
# echo "--------------------------------------------------------------------------
#                            installing Perl Module File::Copy v2.30
# --------------------------------------------------------------------------------
# "
# cpanm File::Copy@$perl_File_Copy_VER
# echo "
# --------------------------------------------------------------------------------
#                           File::Copy v2.30 installed 
# --------------------------------------------------------------------------------
# "
# }

# install_perl_IO_Handle()
# {
# echo "--------------------------------------------------------------------------
#                        installing Perl Module IO::Handle v1.35
# --------------------------------------------------------------------------------
# "
# cpanm IO::Handle@$perl_IO_Handle_VER
# echo "
# --------------------------------------------------------------------------------
#                            IO::Handle v1.35 installed
# --------------------------------------------------------------------------------
# "
# }


# install_perl_Parallel_ForkManager()
# {
# echo "--------------------------------------------------------------------------
#                            installing Perl Module Parallel::ForkManager v1.17
# --------------------------------------------------------------------------------
# "
# cpanm Parallel::ForkManager@$perl_Parllel_ForkManager_VER -l $ROOTDIR/ext
# cpanm Bio::SeqIO -l $ROOTDIR/ext

# echo "
# --------------------------------------------------------------------------------
#                            Parallel::ForkManager v1.17 installed
# --------------------------------------------------------------------------------
# "
# }


################################################################################
if ( checkSystemInstallation conda )
then
  conda_installed_VER=`conda --version 2>&1 | perl -nle 'print $& if m{conda \d+\.\d+\.\d+}'`;
  if ( echo $conda_installed_VER $miniconda_VER | awk '{if($2>=$3) exit 0; else exit 1}' )
  then 
    echo " - found conda $conda_installed_VER"
    if [ -d "$ROOTDIR/thirdParty/miniconda" ]; then
      echo "conda is pointed to right environment"
      echo "creating phame environment"
      conda create --name phame --yes
      source activate phame
    else
      echo "Creating a separate conda enviroment ..."
      conda create --name phame --yes
      source activate phame
    fi
  else
    echo "Required version of conda ($miniconda_VER) was not found"
    install_miniconda
    conda create --name phame --yes
    source activate phame
  fi
else
  echo "conda was not found"
  install_miniconda
  conda create --name phame --yes
  source activate phame
fi

################################################################################
conda install --yes -n phame -c anaconda perl=$perl5_VER 
conda install --yes -n phame -c bioconda perl-app-cpanminus=$cpanm_VER
conda install --yes -n phame -c bioconda mummer=$mummer_VER
conda install --yes -n phame -c bioconda bbmap
conda install --yes -n phame -c anaconda cmake=$cmake_VER
conda install --yes -n phame -c bioconda bwa=$bwa_VER
conda install --yes -n phame -c bioconda bowtie2=$bowtie2_VER
conda install --yes -n phame -c bioconda samtools=$samtools_VER
conda install --yes -n phame -c bioconda FastTree=$FastTree_VER
conda install --yes -n phame -c bioconda RAxML=$RAxML_VER
conda install --yes -n phame -c bioconda muscle=$muscle_VER
conda install --yes -n phame -c bioconda mafft=$mafft_VER
conda install --yes -n phame -c bioconda paml=$paml_VER
conda install --yes -n phame -c bioconda bcftools=$bcftools_VER
cpanm Getopt::Long@$perl_Getopt_Long_VER
cpanm Test::Exception@$perl_Test_Exception_VER
cpanm Statistics::Distributions@$perl_Statistics_Distributions_VER
cpanm Time::HiRes@$perl_Time_HiRes_VER
cpanm File::Path@$perl_File_Path_VER
cpanm File::Basename@$perl_File_Basename_VER
cpanm File::Copy@$perl_File_Copy_VER
# cpanm IO::Handle@$perl_IO_Handle_VER
cpanm Parallel::ForkManager@$perl_Parllel_ForkManager_VER -l $ROOTDIR/ext
cpanm Bio::SeqIO --force
################################################################################
if ( checkHyPhyInstallation HYPHYMP )
then
  hyphy_installed_VER=`thirdParty/hyphy-2.3.11/HYPHYMP -v 2>&1 | grep 'HYPHY' | perl -nle 'print $& if m{HYPHY \d+\.\d+.\d\d}'`;
  if ( echo $hyphy_installed_VER $hyphy_VER | awk '{if($2>=$3) exit 0; else exit 1}' )
  then 
    echo " - found HyPhy $hyphy_installed_VER"
  else 
    echo "Required version of HyPhy $hyphy_VER was not found"
    install_hyphy
  fi
else
  echo "HyPhy was not found"
  install_hyphy
fi


# if ( checkSystemInstallation perl )
# then
#   perl_installed_VER=`perl -v 2>&1| grep 'version' | perl -nle 'print $& if m{\d+\.\d+\.\d+}'`;
#   if  ( echo $perl_installed_VER $perl_VER | awk '{if($1>=$2) exit 0; else exit 1}' )
#   then 
#     echo " - found perl $perl_installed_VER"
#   else
#   echo "Required version of perl $perl_VER was not found"
#   install_perl 
#   fi
# else 
#   echo "perl was not found"
#   install_perl
# fi

# ################################################################################
# if ( checkSystemInstallation cpan )
# then
#     echo " - found cpan"
# else
#   echo "cpan was found"
#   install_cpan
# fi
# ################################################################################
# if ( checkSystemInstallation cpanm )
# then
#   cpanm_installed_VER=`cpanm -V 2>&1| head -n 1 | grep 'version' | perl -nle 'print $& if m{version \d+\.\d+}'`;
#   if  ( echo $cpanm_installed_VER $cpanm_VER | awk '{if($2>=$3) exit 0; else exit 1}' )
#   then 
#     echo " - found cpanm $cpanm_installed_VER"
#   else
#   echo "Required version of cpanm was not found"
#   install_cpanm
#   fi
# else 
#   echo "cpanm was not found"
#   install_cpanm
# fi

# ################################################################################
# if ( checkSystemInstallation cmake )
# then
#   cmake_installed_VER=`cmake -V 2>&1| head -n 1 | grep 'version' | perl -nle 'print $& if m{version \d+\.\d+}'`;
#   if  ( echo $cmake_installed_VER $cmake_VER | awk '{if($2>=$3) exit 0; else exit 1}' )
#   then 
#     echo " - found cmake $cmake_installed_VER"
#   else
#   echo "Required version of cmake was not found"
#   install_cmake
#   fi
# else 
#   echo "cmake was not found"
#   install_cmake
# fi

# ################################################################################
# if ( checkSystemInstallation bbmap.sh )
# then
#   bbmap_installed_VER=`bbmap.sh -v 2>&1| grep 'version' | perl -nle 'print $& if m{version \d+\.\d+}'`;
#   if  ( echo $bbmap_installed_VER $bbmap_VER | awk '{if($2>=$3) exit 0; else exit 1}' )
#   then 
#     echo " - found bbmap $bbmap_installed_VER"
#   else
#   echo "Required version of bbmap was not found"
#   install_bbmap
#   fi
# else 
#   echo "bbmap was not found"
#   install_bbmap
# fi
# ################################################################################
# if ( checkSystemInstallation nucmer )
# then
#   mummer_installed_VER=`nucmer -v 2>&1| grep 'version' | perl -nle 'print $& if m{version \d+\.\d+}'`;
#   if  ( echo $mummer_installed_VER $mummer_VER | awk '{if($2>=$3) exit 0; else exit 1}' )
#   then 
#     echo " - found nucmer $mummer_installed_VER"
#   else
#   echo "Required version of nucmer was not found"
#   install_mummer
#   fi
# else 
#   echo "nucmer was not found"
#   install_mummer
# fi
# ################################################################################

# if ( checkSystemInstallation bwa )
# then
# bwa_installed_VER=`bwa 2>&1| grep 'Version'  | perl -nle 'print $& if m{Version: \d+\.\d+\.\d+}'`;
#   if  ( echo $bwa_installed_VER $bwa_VER | awk '{if($2>=$3) exit 0; else exit 1}' )
#   then
#     echo " - found BWA $bwa_installed_VER"
#   else
#     install_bwa
#   fi
# else
#   echo "bwa is not found"
#   install_bwa
# fi
# ################################################################################

# if ( checkSystemInstallation bowtie2 )
# then
# bowtie2_installed_VER=`bowtie2 --version 2>&1 | grep -v 'Compiler' |grep 'version' | perl -nle 'print $& if m{version \d+\.\d+\.\d+}'`;
#   if (echo $bowtie2_installed_VER $bowtie2_VER | awk '{if($2>=$3) exit 0; else exit 1}' )
#   then
#     echo " - found bowtie2 $bowtie2_installed_VER"
#   else
#     echo "Required version of bowtie2 $bowtie2_VER was not found"
#     install_bowtie2
#   fi
# else
#   echo "bowtie2 is not found"
#   install_bowtie2
# fi
# ################################################################################
# if ( checkSystemInstallation samtools )
# then
#   samtools_installed_VER=`samtools 2>&1| grep 'Version'|perl -nle 'print $& if m{Version: \d+\.\d+.\d+}'`;
#     if ( echo $samtools_installed_VER $samtools_VER| awk '{if($2>=$3) exit 0; else exit 1}' )
#     then
#     echo " - found samtools $samtools_installed_VER"
#     else
#     echo "Required version of samtools $samtools_VER was not found"
#     install_samtools
#     fi
# else
#   install_samtools
# fi
# ################################################################################
# if ( checkSystemInstallation FastTree )
# then
#   FastTree_installed_VER=`FastTree 2>&1| grep 'version'|perl -nle 'print $& if m{version \d+\.\d+.\d+}'`;
#   if ( echo $FastTree_installed_VER $FastTree_VER | awk '{if($2>=$3) exit 0; else exit 1}' )
#   then
#     echo " - found FastTree $FastTree_VER"
#   else
#     echo "Required version of $FastTree_VER was not found"
#     install_FastTree
#   fi
# else
#     echo "FastTree was not found"
#     install_FastTree
# fi

# ################################################################################
# if ( checkSystemInstallation raxmlHPC )
# then
#   RAxMLHPC_installed_VER=`raxmlHPC-PTHREADS -version 2>&1 | grep 'version' | perl -nle 'print $& if m{version \d+\.\d+\.\d+}'`
#   if ( echo $RAxMLHPC_installed_VER $RAxML_VER | awk '{if($2>=$3) exit 0; else exit 1}' )
#   then 
#     echo " - found RAxML $RAxMLHPC_installed_VER"
#   else
#     echo "Required version of $RAxML_VER was not found"
#       install_RAxML
#   fi  
# else
#   echo "RAxML was not found"
#   install_RAxML
# fi

# ################################################################################
# if ( checkSystemInstallation muscle )
# then
# muscle_installed_VER=`muscle -version 2>&1 | grep 'v' | perl -nle 'print $& if m{v\d+\.\d+\.\d+}'`;
#   if ( echo $muscle_installed_VER $muscle_VER | awk '{if($2>=$3) exit 0; else exit 1}' )
#   then
#     echo " - found muscle $muscle_installed_VER"
#   else
#     echo "Required version of $muscle_VER was not found"
#     install_muscle
#   fi
# else
#   echo "muscle was not found"
#   install_muscle
# fi

# ################################################################################
# if ( checkSystemInstallation mafft )
# then
#   mafft_installed_VER=`mafft --version 2>&1 | grep 'v' | perl -nle 'print $& if m{v\d+\.\d+}'`;
#   if ( echo $mafft_installed_VER $mafft_VER | awk '{if($2>=$3) exit 0; else exit 1}' )
#   then 
#     echo " - found mafft $mafft_installed_VER"  
#   else
#   echo "Required version of mafft $mafft_VER was not found"
#   install_mafft
#   fi
# else
#   echo "mafft was not found"
#   install_mafft
# fi


# ################################################################################
# if ( checkSystemInstallation bcftools )
# then
#   bcftools_installed_VER=`bcftools -v 2>&1| grep 'bcftools' | perl -nle 'print $& if m{\d+\.\d+}'`;
#   if  ( echo $bcftools_installed_VER $bcftools_VER | awk '{if($2>=$3) exit 0; else exit 1}' )
#   then 
#     echo " - found bcftools $bcftools_installed_VER"
#   else
#   echo "Required version of bcftools was not found"
#   install_bcftools
#   fi
# else 
#   echo "bcftools was not found"
#   install_bcftools
# fi
# ################################################################################
# if ( checkSystemInstallation codeml )
# then
#   paml_installed_VER=`evolver \0 2>&1 | grep 'version' | perl -nle 'print $& if m{version \d+\.\d+}'`;
#   if ( echo $paml_installed_VER $paml_VER | awk '{if($2>=$3) exit 0; else exit 1}' )
#   then 
#     echo " - found paml $paml_installed_VER"
#   else 
#     echo "Required version of paml $paml_VER was not found"
#     install_paml
#   fi
# else
#   echo "paml is not found"
#   install_paml
# fi

# ################################################################################
# if ( checkHyPhyInstallation HYPHYMP )
# then
#   hyphy_installed_VER=`thirdParty/hyphy-2.3.11/HYPHYMP -v 2>&1 | grep 'HYPHY' | perl -nle 'print $& if m{HYPHY \d+\.\d+.\d\d}'`;
#   if ( echo $hyphy_installed_VER $hyphy_VER | awk '{if($2>=$3) exit 0; else exit 1}' )
#   then 
#     echo " - found HyPhy $hyphy_installed_VER"
#   else 
#     echo "Required version of HyPhy $hyphy_VER was not found"
#     install_hyphy
#   fi
# else
#   echo "HyPhy was not found"
#   install_hyphy
# fi

# ################################################################################
# #                                 Perl modules
# ################################################################################

# if ( checkPerlModule Getopt::Long )
# then
#   echo " - found Perl module Getopt::Long"
#   perl_Getopt_Long_installed_VER=`perl -MGetopt::Long -e 'print $Getopt::Long::VERSION ."\n";'`
#   if ( echo $perl_Getopt_Long_installed_VER $perl_Getopt_Long_VER | awk '{if($2>=$3) exit 0; else exit 1}')
#   then
#     echo " - found Perl module Getopt::Long $perl_Getopt_Long_installed_VER"
#   else
#     echo "Required version of Getopt::Long $perl_Getopt_Long_VER was not found"
#     install_perl_Getopt_Long
#   fi
# else
#   echo "Perl Getopt::Long was not found"
#   install_perl_Getopt_Long
# fi

# #------------------------------------------------------------------------------#

# if ( checkPerlModule Time::HiRes )
# then
#   perl_Time_HiRes_installed_VER=`perl -MTime::HiRes -e 'print $Time::HiRes::VERSION ."\n";'`
#   if ( echo $perl_Time_HiRes_installed_VER $perl_Time_HiReS_VER | awk '{if($2>=$3) exit 0; else exit 1}')
#   then
#     echo " - found Perl module Time::HiRes $perl_Time_HiRes_installed_VER"
#   else
#     echo "Required version of Time::HiRes $perl_Time_HiRes_VER was not found"
#     install_perl_Time_HiRes
#   fi
# else
#   echo "Perl Time::HiRes was not found"
#   install_perl_Time_HiRes
# fi
# #------------------------------------------------------------------------------#
# if ( checkPerlModule File::Path )
# then
#   perl_File_Path_installed_VER=`perl -MFile::Path -e 'print $File::Path::VERSION ."\n";'`
#   if ( echo $perl_File_Path_installed_VER $perl_File_Path_VER | awk '{if($2>=$3) exit 0; else exit 1}')
#   then
#     echo " - found Perl module File::Path $perl_File_Path_installed_VER"
#   else
#     echo "Required version of File::Path $perl_File_Path_VER was not found"
#     install_perl_File_Path
#   fi
# else
#   echo "Perl File::Path is not found"
#   install_perl_File_Path
# fi
# #------------------------------------------------------------------------------#
# if ( checkPerlModule File::Basename )
# then
#   perl_File_BaseName_installed_VER=`perl -MFile::Basename -e 'print $File::Basename::VERSION ."\n";'`
#   if ( echo $perl_File_BaseName_installed_VER $perl_File_BaseName_VER | awk '{if($2>=$3) exit 0; else exit 1}')
#   then
#     echo " - found Perl module File::BaseName $perl_File_BaseName_installed_VER"
#   else
#     echo "Required version of File::BaseName $perl_File_BaseName_VER was not found"
#     install_perl_File_BaseName
#   fi
# else
#   echo "Perl File::Basename is not found"
#   install_perl_File_Basename
# fi
# #------------------------------------------------------------------------------#
# if ( checkPerlModule File::Copy )
# then
#   perl_File_Copy_installed_VER=`perl -MFile::Copy -e 'print $File::Copy::VERSION ."\n";'`
#   if ( echo $perl_File_Copy_installed_VER $perl_File_Copy_VER | awk '{if($2>=$3) exit 0; else exit 1}')
#   then
#     echo " - found Perl module File::Copy $perl_File_Copy_installed_VER"
#   else
#     echo "Required version of File::Copy $perl_File_Copy_VER was not found"
#     install_perl_File_Copy
#   fi
# else
#   echo "Perl File::Copy is not found"
#   install_perl_File_Copy
# fi
# #------------------------------------------------------------------------------#
# # if ( checkPerlModule IO::Handle )
# # then
# #   #perl -MIO::Handle -e 'print $IO::Handle::VERSION ."\n";'
# #   perl_IO_Handle_installed_VER=`perl -MIO::Handle -e 'print $IO::Handle::VERSION ."\n";'`
# #   if ( echo $perl_IO_Handle_installed_VER $perl_IO_Handle_VER | awk '{if($2>=$3) exit 0; else exit 1}')
# #   then
# #     echo " - found Perl module IO::Handle $perl_IO_Handle_installed_VER"
# #   else
# #     echo "Required version of IO::Handle $perl_IO_Handle_VER was not found"
# #     install_perl_IO_Handle
# #   fi
# # else
# #   echo "Perl IO::Handle is not found"
# #   install_perl_IO_Handle
# # fi
# #------------------------------------------------------------------------------#
# if ( checkPerlModule Test::Exception )
# then
#   #perl -MTest::Exception -e 'print $Test::Exception::VERSION ."\n";'
#   perl_Test_Exception_installed_VER=`perl -MTest::Exception -e 'print $Test::Exception::VERSION ."\n";'`
#   if ( echo $perl_Test_Exception_installed_VER $perl_Test_Exception_VER | awk '{if($2>=$3) exit 0; else exit 1}')
#   then
#     echo " - found Perl module Test::Exception $perl_Test_Exception_installed_VER"
#   else
#     echo "Required version of Test::Exception $perl_Test_Exception_VER was not found"
#     install_perl_Test_Exception
#   fi
# else
#   echo "Perl Test::Exception is not found"
#   install_perl_Test_Exception
# fi
# #------------------------------------------------------------------------------#
# # if ( checkPerlModule Parallel::ForkManager )
# # then
# #   perl_Parallel_ForkManager_installed_VER=`perl -MParallel::ForkManager -e 'print $Parallel::ForkManager::VERSION ."\n";'`
# #   if ( echo $perl_Parallel_ForkManager_installed_VER $perl_Parallel_ForkManager_VER | awk '{if($1>=$2) exit 0; else exit 1}')
# #   then
# #     echo " - found Perl module Parallel::ForkManager $perl_Parallel_ForkManager_installed_VER"
# #   else
# #     echo "Required version of Parallel::ForkManager $perl_Parallel_ForkManager_VER was not found"
# #     install_perl_Parallel_ForkManager
# #   fi
# # else
# #   echo "Perl Parallel::ForkManager is not found"
# #   install_perl_Parallel_ForkManager
# # fi
# #------------------------------------------------------------------------------#
# if ( checkPerlModule Statistics::Distributions )
# then
#   perl_Statistics_Distributions_installed_VER=`cpan -D Statistics::Distributions 2>&1 | grep 'Installed' | perl -nle 'print $& if m{Installed: \d+\.\d+}'`
#   if ( echo $perl_Statistics_Distributions_installed_VER $perl_Statistics_Distributions_VER | awk '{if($2>=$3) exit 0; else exit 1}')
#   then
#     echo " - found Perl module Statistics::Distributions $perl_Statistics_Distributions_installed_VER"
#   else
#     echo "Required version of Statistics::Distributions $perl_Statistics_Distributions_VER was not found"
#     install_perl_Statistics_Distributions
#   fi
# else
#   echo "Perl Statistics::Distributions is not found"
#   install_perl_Statistics_Distributions
# fi

################################################################################




################################################################################
echo "
================================================================================
                 PhaME installed successfully.
================================================================================
Check phame.ctl for the control file

Quick test:
    cd PhaME-1
    sh test/TestAll.sh
    Please use the full path to specify the location of fasta file.
    Read README.md for detail
Check our github site for update:
    https://github.com/mshakya/PhaME-1
";