setup.sh

#!/bin/bash

########## LICENSE ##########
# Copyright (c) 2016-2021 Genome Research Ltd.
#
# Author: Cancer Genome Project cgphelp@sanger.ac.uk
#
# This file is part of cgpBigWig.
#
# cgpBigWig 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_HTSLIB="1.20"
export VER_LIBBW="0.4.6"
export VER_LIBDEFLATE="v1.6"

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/cgpPinel-X.X.X /opt/cgpVcf-X.X.X/lib/perl:/opt/PCAP-core-X.X.X/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

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

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