setup.sh

#!/bin/bash

##########LICENCE##########
# Copyright (c) 2014-2020 Genome Research Ltd.,
#
# This file is part of cgpVAF.
#
# cgpVaf is free software: you can redistribute it and/or modify it under
# the terms of the GNU Affero General Public License as published by the Free
# Software Foundation; either version 3 of the License, or (at your option) any
# later version.
#
# This program is distributed in the hope that it will be useful, but WITHOUT
# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
# FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more
# details.
#
# You should have received a copy of the GNU Affero General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
##########LICENCE##########

SOURCE_VCFTOOLS="https://github.com/vcftools/vcftools/releases/download/v0.1.16/vcftools-0.1.16.tar.gz"
SOURCE_BIOBDHTS="https://github.com/Ensembl/Bio-HTS/archive/2.11.tar.gz"
SOURCE_HTSLIB="https://github.com/samtools/htslib/releases/download/1.9/htslib-1.9.tar.bz2"
SOURCE_SAMTOOLS="https://github.com/samtools/samtools/releases/download/1.7/samtools-1.9.tar.bz2"
SOURCE_EXONERATE="http://ftp.ebi.ac.uk/pub/software/vertebrategenomics/exonerate/exonerate-2.2.0.tar.gz"

get_distro () {
  EXT=""
  DECOMP="gunzip -f"
  if [[ $2 == *.tar.bz2* ]] ; then
    EXT="tar.bz2"
    DECOMP="bzip2 -fd"
  elif [[ $2 == *.tar.gz* ]] ; then
    EXT="tar.gz"
  else
    echo "I don't understand the file type for $1"
    exit 1
  fi
  rm -f $1.$EXT
  if hash curl 2>/dev/null; then
    curl --retry 10 -sS -o $1.$EXT -L $2
  else
    wget --tries=10 -nv -O $1.$EXT $2
  fi
}

get_file () {
# output, source
  if hash curl 2>/dev/null; then
    curl --insecure -sS -o $1 -L $2
  else
    wget -nv -O $1 $2
  fi
}

if [[ ($# -lt 1) ]] ; then
  echo "Please provide an installation path and optional value to prevent install of dependencies, e.g."
  echo "  ./setup.sh /opt/myBundle"
  echo "OR to skip install of samtools, vcftools and exonerate:"
  echo "  ./setup.sh /opt/myBundle 1"
  exit 0
fi

CPU=`grep -c ^processor /proc/cpuinfo`
if [ $? -eq 0 ]; then
  if [ "$CPU" -gt "6" ]; then
    CPU=6
  fi
else
  CPU=1
fi
echo "Max compilation CPUs set to $CPU"

INST_PATH=$1

if [[ "x$2" == "x" ]] ; then
  INST_METHOD=0
else
  INST_METHOD=$2
fi


# get current directory
INIT_DIR=`pwd`

echo > $INIT_DIR/setup.log

# create inst_path
mkdir -p $INST_PATH/bin
mkdir -p $INST_PATH/lib
mkdir -p $INST_PATH/config
mkdir -p $INST_PATH/bin/hdr
cp $INIT_DIR/perl/config/log4perl.vaf.conf $INST_PATH/config/
cp -rp $INIT_DIR/README.md	$INST_PATH/README.md

cd $INST_PATH
INST_PATH=`pwd`
cd $INIT_DIR

# make sure that build is self contained
unset PERL5LIB
PERLROOT=$INST_PATH/lib/perl5
export PERL5LIB="$PERLROOT"

# log information about this system
echo '============== System information ===='
set -x
lsb_release -a
uname -a
sw_vers
system_profiler
grep MemTotal /proc/meminfo
set +x
echo

set -e

#create a location to build dependencies
SETUP_DIR=$INIT_DIR/install_tmp
mkdir -p $SETUP_DIR

cd $SETUP_DIR

if [ $INST_METHOD -gt 0 ] ; then
  echo -e "\n\t !!! Not installing additional tools: as requested !!! \n"
fi

perlmods=( "File::ShareDir" "File::ShareDir::Install" "XML::DOM::XPath" "Bio::Root::Version" "Module::Build~0.42" )
echo "Building perl requirements ..."
if [ -e $SETUP_DIR/perl-mods.success ]; then
  echo " already built ...";
else
  for i in "${perlmods[@]}" ; do
    echo "Installing build prerequisite $i..."
      set -x
      cpanm -v --mirror http://cpan.metacpan.org --notest -l $INST_PATH $i
      set +x
      echo; echo
  done
  touch $SETUP_DIR/perl-mods.success
fi


echo "Getting htslib ..."
if [ -e $SETUP_DIR/htslibGet.success ]; then
  echo " already staged ...";
else
  cd $SETUP_DIR
  get_distro "htslib" $SOURCE_HTSLIB
  touch $SETUP_DIR/htslibGet.success
fi


echo "Building htslib ..."
if [ -e $SETUP_DIR/htslib.success ]; then
  echo " previously installed ...";
else
  (
  mkdir -p htslib
  tar --strip-components 1 -C htslib -jxf htslib.tar.bz2
  cd htslib
  ./configure --enable-plugins --enable-libcurl --prefix=$INST_PATH
  make -s -j$CPU
  make install
  cd $SETUP_DIR
  touch $SETUP_DIR/htslib.success
  ) >/dev/null
fi

export HTSLIB=$INST_PATH
echo "Building Bio::DB::HTS ..."
if [ -e $SETUP_DIR/biohts.success ]; then
  echo " previously installed ...";
else
  echo
  cd $SETUP_DIR
  rm -rf bioDbHts
  get_distro "bioDbHts" $SOURCE_BIOBDHTS
  mkdir -p bioDbHts
  tar --strip-components 1 -C bioDbHts -zxf bioDbHts.tar.gz
  cd bioDbHts
  perl Build.PL --htslib=$HTSLIB --install_base=$INST_PATH
  ./Build
  ./Build test
  ./Build install
  cd $SETUP_DIR
  rm -f bioDbHts.tar.gz
  touch $SETUP_DIR/biohts.success
fi

CURR_TOOL="vcftools"
CURR_SOURCE=$SOURCE_VCFTOOLS
echo -n "Building $CURR_TOOL ..."
if [ -e $SETUP_DIR/$CURR_TOOL.success ]; then
  echo -n " previously installed ..."
else
  cd $SETUP_DIR
  mkdir -p $SETUP_DIR/distro
  curl -sSL --retry 10 $SOURCE_VCFTOOLS > distro.tar.gz
  rm -rf distro/*
  tar --strip-components 2 -C distro -xzf distro.tar.gz
  cd $SETUP_DIR/distro
  ./configure --prefix=$INST_PATH --with-pmdir=lib/perl5
  make -j$CPU
  make -j$CPU install
  cd $SETUP_DIR
  rm -rf distro/* distro.*
  touch $SETUP_DIR/$CURR_TOOL.success
fi

if [ $INST_METHOD -lt 2 ] ; then
  if [[ ",$COMPILE," == *,samtools,* ]] ; then
    echo "Building samtools ..."
    if [ -e $SETUP_DIR/samtools.success ]; then
      echo " previously installed ...";
    else
      cd $SETUP_DIR
      rm -rf samtools
      get_distro "samtools" $SOURCE_SAMTOOLS
      mkdir -p samtools
      tar --strip-components 1 -C samtools -xjf samtools.tar.bz2
      cd samtools
      ./configure --enable-plugins --enable-libcurl --prefix=$INST_PATH
      make -s -j$CPU all all-htslib
      make install all all-htslib
      cd $SETUP_DIR
      rm -f samtools.tar.bz2
      touch $SETUP_DIR/samtools.success
    fi
  else
    echo "samtools - No change between vafCorrect versions"
  fi

  CURR_TOOL="exonerate"
  CURR_SOURCE=$SOURCE_EXONERATE
  echo -n "Building exonerate..."
  if [ -e $SETUP_DIR/$CURR_TOOL.success ]; then
    echo -n " previously installed ..."
  elif [ $INST_METHOD -eq 2 ]; then
    echo " Skipping exonerate install ..."
  else
    cd $SETUP_DIR
    set -x
    get_distro $CURR_TOOL $CURR_SOURCE
    tar zxf exonerate.tar.gz
    cd exonerate-2.2.0
    cp $INIT_DIR/patches/exonerate_pthread-asneeded.diff .
    patch -p1 < exonerate_pthread-asneeded.diff
    ./configure --prefix=$INST_PATH
    make -s
    make check
    make install
    cd $INIT_DIR
    touch $SETUP_DIR/exonerate.success
  fi
fi

export PATH=$PATH:$INST_PATH/bin
export PERL5LIB=$PERL5LIB:$PERLROOT:$PERLARCH

cd "$INIT_DIR/perl"

echo -n "Installing Perl prerequisites ..."
if ! ( perl -MExtUtils::MakeMaker -e 1 >/dev/null 2>&1); then
    echo
    echo "WARNING: Your Perl installation does not seem to include a complete set of core modules.  Attempting to cope with this, but if installation fails please make sure that at least ExtUtils::MakeMaker is installed.  For most users, the best way to do this is to use your system's package manager: apt, yum, fink, homebrew, or similar."
fi

set -x
cpanm -v --mirror http://cpan.metacpan.org --notest -l $INST_PATH --installdeps . < /dev/null
set +x

echo -n "Installing cgpVaf ..."
cd "$INIT_DIR/perl"
echo -n `pwd`
perl Makefile.PL INSTALL_BASE=$INST_PATH
make
make test
make install

# cleanup all junk
rm -rf $SETUP_DIR

echo
echo
echo "Please add the following to beginning of PATH:"
echo "  $INST_PATH/bin"
echo "Please add the following to beginning of PERL5LIB:"
echo "  $PERLROOT"
echo "  $PERLARCH"
echo

exit 0