setup.sh

#!/bin/bash

########## LICENSE ##########
# Copyright (c) 2014-2020 Genome Research Ltd.
#
# Author: CASM/Cancer IT <cgphelp@sanger.ac.uk>
#
# This file is part of AscatNGS.
#
# AscatNGS 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/>.
#
#    1. The usage of a range of years within a copyright statement contained within
#    this distribution should be interpreted as being equivalent to a list of years
#    including the first and last year specified and all consecutive years between
#    them. For example, a copyright statement that reads ‘Copyright (c) 2005, 2007-
#    2009, 2011-2012’ should be interpreted as being identical to a statement that
#    reads ‘Copyright (c) 2005, 2007, 2008, 2009, 2011, 2012’ and a copyright
#    statement that reads ‘Copyright (c) 2005-2012’ should be interpreted as being
#    identical to a statement that reads ‘Copyright (c) 2005, 2006, 2007, 2008,
#    2009, 2010, 2011, 2012’."
#
###########################

# ALL tool versions used by opt-build.sh
# need to keep in sync with Dockerfile
export VER_CGPVCF="v2.2.1"
export VER_VCFTOOLS="0.1.16"
export VER_ALLELECOUNT="v4.2.1"

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


if [[ ($# -ne 1 && $# -ne 2) ]] ; then
  echo "Please provide an installation path and optionally perl lib paths to allow, e.g."
  echo "  ./setup.sh /opt/myBundle"
  echo "OR all elements versioned:"
  echo "  ./setup.sh /opt/cgpVcf-X.X.X /opt/PCAP-X.X.X/lib/perl:/some/other/lib/perl..."
  exit 1
fi

INST_PATH=$1

if [[ $# -eq 2 ]] ; then
  CGP_PERLLIBS=$2
fi

# get current directory
INIT_DIR=`pwd`

set -e

# cleanup inst_path
mkdir -p $INST_PATH/bin
cd $INST_PATH
INST_PATH=`pwd`
cd $INIT_DIR

# make sure that build is self contained
PERLROOT=$INST_PATH/lib/perl5

# allows user to knowingly specify other PERL5LIB areas.
if [ -z ${CGP_PERLLIBS+x} ]; then
  PERL5LIB="$PERLROOT"
else
  PERL5LIB="$PERLROOT:$CGP_PERLLIBS"
fi

export PERL5LIB=$PERL5LIB

#add bin path for install tests
export PATH=$INST_PATH/bin:$PATH

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

#install cpanm
get_file $SETUP_DIR/cpanm https://cpanmin.us/
perl $SETUP_DIR/cpanm -l $INST_PATH App::cpanminus

#install R stuff
export R_LIBS=$INST_PATH/R-libs
export R_LIBS_USER=$INST_PATH/R-libs
mkdir -p $R_LIBS_USER
Rscript build/libInstall.R $R_LIBS_USER 2>&1 | grep '^\*'
bash build/opt-build.sh $INST_PATH
bash build/opt-build-local.sh $INST_PATH

echo
echo
echo "Please add the following to beginning of path:"
echo "  $INST_PATH/bin"
echo

exit 0