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SETUP_VM.md

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Setup genenetwork on CentOS 6.9

VM setup on CentOS 6.9.

Install NodeJS

We need to install nodejs and npm to run this application on CentOS.

yum install nodejs
npm install n
npm n stable

Install the right version of GCLIB

http://luiarthur.github.io/gccinstall

Download the right gcc version from the internet.

cd /opt
wget http://www.netgull.com/gcc/releases/gcc-5.2.0/gcc-5.2.0.tar.gz
tar -xvf gcc-5.2.0.tar.gz
ln -s gcc-5.2.0 gcc

Create a directory to run make and make install to compile gcc module

cd /opt
mkdir objdir
$PWD/../gcc/configure --prefix=/opt/gcc --enable-languages=c,c++,fortran,go --disable-multilib
# note this takes several hours
nohup make &
nohup make install &

Add the following content to the root-profile and molgenis profile:

  • vi /root/.bashrc
  • vi /srv/molgenis/.bashrc
export PATH=/opt/gcc/bin:$PATH
export LD_LIBRARY_PATH=/opt/gcc/lib:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH=/opt/gcc/lib64:$LD_LIBRARY_PATH

Packaging

TODO:

  • Need to release this project with npm version in new release train (https://jenkins.dev.molgenis.org)
  • Need to have a Docker image to roil out on new kubernetes cluster
  • Upgrade elasticsearch to at least 5.5.1
  • Create helm-chart for kubernetes cluster