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#!/bin/bash
# The MIT License (MIT)
# Copyright (c) 2019-2021 Omics Data Automation, Inc.
# Copyright (c) 2023 dātma, inc™
#
# Permission is hereby granted, free of charge, to any person obtaining a copy of
# this software and associated documentation files (the "Software"), to deal in
# the Software without restriction, including without limitation the rights to
# use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
# the Software, and to permit persons to whom the Software is furnished to do so,
# subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in all
# copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
# FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
# COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
# IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
# CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
#
install_devtoolset() {
echo "Installing devtoolset"
if [[ $CENTOS_VERSION -ge 8 ]]; then
yum -y makecache &&
yum -y grouplist &&
yum -y groupinstall "Development Tools"
else
yum install -y centos-release-scl &&
yum install -y devtoolset-7 &&
echo "source /opt/rh/devtoolset-7/enable" >> $PREREQS_ENV
fi
}
install_cmake3() {
CMAKE=`which cmake`
if [[ ! -z $CMAKE ]]; then
CMAKE_VERSION=$($CMAKE -version | awk '/version/{print $3}')
fi
if [[ -z $CMAKE_VERSION || CMAKE_VERSION < "3.6" ]]; then
echo "Installing cmake..."
wget -nv https://github.com/Kitware/CMake/releases/download/v3.19.1/cmake-3.19.1-Linux-x86_64.sh -P /tmp &&
chmod +x /tmp/cmake-3.19.1-Linux-x86_64.sh &&
/tmp/cmake-3.19.1-Linux-x86_64.sh --prefix=/usr/local --skip-license
if [ ! -f /usr/local/bin/cmake3 ]; then
ln -s /usr/local/bin/cmake /usr/local/bin/cmake3
fi
fi
}
install_openjdk() {
if [[ $CENTOS_VERSION -ge 8 ]]; then
echo "Installing openjdk" &&
yum install -y -q java-17-openjdk-devel &&
echo "export JRE_HOME=/usr/lib/jvm/jre" >> $PREREQS_ENV
else
curl -O https://download.java.net/java/GA/jdk17.0.2/dfd4a8d0985749f896bed50d7138ee7f/8/GPL/openjdk-17.0.2_linux-x64_bin.tar.gz &&
tar zxvf openjdk-17.0.2_linux-x64_bin.tar.gz &&
mv jdk-17.0.2 /usr/local/ &&
echo "export JAVA_HOME=/usr/local/jdk-17.0.2" >> $PREREQS_ENV
fi
}
install_mpi() {
yum install -y -q mpich-devel &&
echo "export PATH=/usr/lib64/mpich/bin:\$PATH" >> $PREREQS_ENV &&
echo "export LD_LIBRARY_PATH=/usr/lib64:/usr/lib:\$LD_LIBRARY_PATH" >> $PREREQS_ENV
}
install_csv() {
if [[ $CENTOS_VERSION -lt 8 ]]; then
yum install -y -q libcsv libcsv-devel &&
yum install -y -q csv
fi
}
# Sufficient to build/install the genomicsdb libraries
install_minimum_prerequisites() {
yum install -y -q deltarpm
yum update -y -q &&
yum install -y -q epel-release &&
yum install -y -q which wget git &&
yum install -y -q autoconf automake libtool unzip &&
yum install -y -q cmake3 patch &&
yum install -y -q perl perl-IPC-Cmd &&
yum install -y -q libuuid libuuid-devel &&
yum install -y -q curl libcurl-devel
}
install_openssl() {
OPENSSL_PREFIX=$INSTALL_PREFIX/ssl
if [[ ! -d $OPENSSL_PREFIX ]]; then
echo "Installing OpenSSL"
pushd /tmp
wget $WGET_NO_CERTIFICATE https://www.openssl.org/source/openssl-$OPENSSL_VERSION.tar.gz &&
tar -xvzf openssl-$OPENSSL_VERSION.tar.gz &&
cd openssl-$OPENSSL_VERSION &&
CFLAGS=-fPIC ./config -fPIC no-shared --prefix=$OPENSSL_PREFIX --openssldir=$OPENSSL_PREFIX &&
make && make install && echo "Installing OpenSSL DONE"
rm -fr /tmp/openssl*
popd
fi
add_to_env OPENSSL_ROOT_DIR $OPENSSL_PREFIX
add_to_env LD_LIBRARY_PATH $OPENSSL_PREFIX/lib
}
install_system_prerequisites() {
yum install -y -q deltarpm
yum update -y -q &&
yum install -y -q sudo &&
yum install -y -q which wget git make &&
install_mpi &&
install_devtoolset &&
install_openjdk &&
yum install -y -q autoconf automake libtool unzip &&
yum update -y -q autoconf &&
yum install -y -q epel-release &&
yum install -y zlib-devel &&
yum install -y -q openssl-devel &&
install_cmake3 &&
yum install -y -q libuuid libuuid-devel &&
yum install -y -q patch &&
yum install -y -q zstd &&
yum install -y -q curl libcurl-devel &&
install_csv
}
install_nobuild_prerequisites() {
yum install -y -q deltarpm
yum update -y -q &&
install_mpi &&
yum install -y -q epel-release &&
yum install -y zlib-devel &&
yum install -y -q openssl-devel &&
yum install -y -q cmake3 &&
yum install -y -q patch &&
yum install -y -q libuuid libuuid-devel &&
yum install -y -q zstd &&
yum install -y -q curl libcurl-devel
}
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