Set up Ensembl v84 REST API on CentOS 6.7

ensembl_rest_on_centos6.sh

#!/bin/bash

# GOAL: Set up a local instance of Ensembl's database and REST API

# If I don't already have sudo rights, then first login as root with `su`, and type `visudo` to
# edit `/etc/sudoers`, and uncomment this line in that file:
# %wheel ALL=(ALL) ALL
# This allows any user in group `wheel` to use `sudo`. Add myself to the `wheel` group using:
# usermod -a -G wheel kandoth
# Also set `SELINUX=disabled` in `/etc/selinux/config`, because its a PITFA.
# Run `reboot` and login again, to set changes above, before proceeding with commands below.

# Update all apps:
sudo yum update -y

# Install some bare essentials:
sudo yum install -y epel-release
sudo yum groupinstall -y 'Development Tools'
sudo yum install -y cmake vim R perl-devel python-devel zlib-devel bzip2-devel expat-devel libxml2-devel openssl-devel mysql-devel

# Make a folder where we can set up perl and cd into it:
export PERLBASE=/opt/common/CentOS_6-dev/perl
mkdir -p $PERLBASE
cd $PERLBASE

# Download and untar latest source tarball into subfolder src:
wget -P src http://www.cpan.org/src/5.0/perl-5.24.0.tar.gz
tar -zxf src/perl-5.24.0.tar.gz

# Configure and build:
cd perl-5.24.0
./Configure -des -Dprefix=/opt/common/CentOS_6-dev/perl/perl-5.24.0 -Dotherlibdirs=/opt/common/CentOS_6-dev/perl/perl-5.24.0/lib/perl5
make && make install
cd ..

# Override the system Perl with this Perl:
export PATH=$PERLBASE/perl-5.24.0/bin:$PATH

# Install dependencies for Ensembl and other tools we use:
curl -L http://cpanmin.us | /opt/common/CentOS_6-dev/perl/perl-5.24.0/bin/perl - --notest -l /opt/common/CentOS_6-dev/perl/perl-5.24.0 App::cpanminus JSON::Parse XML::Parser XML::Simple Encode DBD::mysql LWP LWP::Protocol::https Archive::Extract Archive::Tar Archive::Zip CGI DBI Time::HiRes Statistics::R Statistics::Lite Tie::Autotie Tie::IxHash Log::Log4perl FindBin::Real Getopt::Long Catalyst::Runtime Catalyst::Devel List::Util Test::XML::Simple Test::XPath IO::String Bio::Perl

# Force delete the older List::Util so that the one installed above by cpanm is used instead:
rm -rf /opt/common/CentOS_6-dev/perl/perl-5.24.0/lib/{,5.24.0/x86_64-linux/}{List,auto/List}

# Download Ensembl's git tools, and add it to PATH:
cd src
git clone https://github.com/Ensembl/ensembl-git-tools.git
export PATH=$PERLBASE/src/ensembl-git-tools/bin:$PATH

# Install all the Ensembl Perl APIs using the git ensembl command:
git ensembl --clone api

# Clone and build tabix, then install the Perl module:
git clone https://github.com/samtools/tabix.git
(cd tabix && make)
(cd tabix/perl && perl Makefile.PL && make && make install)

# Add tabix to PATH and have LD_LIBRARY_PATH point to its libs:
export PATH=$PERLBASE/src/tabix:$PATH
export LD_LIBRARY_PATH=$PERLBASE/src/tabix

# Set up environment as described in the basic installation instructions.
PERL5LIB=$PERLBASE/src/ensembl/modules
PERL5LIB=${PERL5LIB}:$PERLBASE/src/ensembl-compara/modules
PERL5LIB=${PERL5LIB}:$PERLBASE/src/ensembl-funcgen/modules
PERL5LIB=${PERL5LIB}:$PERLBASE/src/ensembl-io/modules
PERL5LIB=${PERL5LIB}:$PERLBASE/src/ensembl-variation/modules
export PERL5LIB

# Install Bio::DB::HTS::Faidx which needs htslib libraries:
git clone https://github.com/samtools/htslib.git
(cd htslib && make)
export HTSLIB_DIR=$PERLBASE/src/htslib
cpanm --notest -l /opt/common/CentOS_6-dev/perl/perl-5.24.0 Bio::DB::HTS::Faidx

# Clone and install ensembl-rest:
git clone https://github.com/Ensembl/ensembl-rest.git
cd ensembl-rest
cpanm --installdeps --notest .
perl Makefile.PL
cd ..

# Make sure we can ping the ensembl server:
perl ensembl/misc-scripts/ping_ensembl.pl

# Make a copy of the server config, and point it to the useastdb:
cp ensembl-rest/ensembl_rest.conf.default ensembl-rest/ensembl_rest.conf
perl -i -pe 's/ensembldb/useastdb/' ensembl-rest/ensembl_rest.conf

# Point the server to the config, and startup:
export ENSEMBL_REST_CONFIG=$PERLBASE/src/ensembl-rest/ensembl_rest.conf
nohup perl ensembl-rest/script/ensembl_rest_server.pl > ensembl_rest_server.log 2>&1 &

# Test that we can ping the REST service:
curl -L http://172.21.75.56:3000/info/ping?content-type=application/json