Cyverse_Setup

A repository for documentation about how the Cyverse VM was set up.

Installed programs

The VM runs CentOS7, but comes as a clean install. A number of programs need to be installed. The first set of commands will show got to install the programs needed to set up the current configuration:

sudo yum update
sudo yum upgrade
sudo yum install R git nano libcurl-devel libxml2-devel time -y

The package libcurl-devel is used in the httr and curl R packages that we will install later. libxml2-devel is used in the xml2 package.

Docker

Docker required some additional configuration:

sudo yum install -y yum-utils \
  device-mapper-persistent-data \
  lvm2

sudo yum-config-manager \
    --add-repo \
    https://download.docker.com/linux/centos/docker-ce.repo

sudo yum install docker-ce -y

To install docker-compose for some of the work we use:

sudo curl -L https://github.com/docker/compose/releases/download/1.18.0/docker-compose-`uname -s`-`uname -m` -o /usr/local/bin/docker-compose
sudo chmod +x /usr/local/bin/docker-compose

This allows us to use docker-compose files in other repositories to facilitate some of our development workflows.

I've added myself to a docker group:

sudo groupadd docker
sudo usermod -aG docker $USER
sudo systemctl enable docker

Then start the docker system up:

sudo systemctl start docker 

This should happen on startup (having run , but if you get errors then use that command.

neo4j

To install neo4j, the graph database used in this project:

sudo su
rpm --import http://debian.neo4j.org/neotechnology.gpg.key
cat <<EOF>  /etc/yum.repos.d/neo4j.repo
[neo4j]
name=Neo4j RPM Repository
baseurl=http://yum.neo4j.org/stable
enabled=1
gpgcheck=1
EOF

Then install as normal:

sudo yum install neo4j-3.3.0

At this point everything is installed.

Setting up the neo4j Service

Following installation:

The neo4j Documentation provides a guide to Linux file Locations for reference.

Set the Admin Password

Before running neo4j for the first time you need to set the admin password (and then start the service):

sudo neo4j-admin set-initial-password <yourpasswordhere>
sudo service neo4j start

Add APOC Plugins

The APOC plugins allow us to parse XML files for the NSF awards, to add them to the larger graph database. They are installed by downloading the latest version of the jar package:

sudo curl -o /var/lib/neo4j/plugins/apoc-3.2.3.5-all.jar "https://github.com/neo4j-contrib/neo4j-apoc-procedures/releases/download/3.2.3.5/apoc-3.2.3.5-all.jar"

Setting up Remote Access

Documentation how to set up remote access for the neo4j server is provided.

it etc/neo4j/conf/neo4j.conf to change dbms.connector.https.address=0.0.0.0:7473

Then access the server using the Cyverse host's IP address (using hostname -I). Note that a firewall exception must be made.

Installing R

Given the R installation above, the following packages have been required:

Rscript -e "install.packages(c('RNeo4j', 'httr', 'readr', 'dplyr', 'curl', 'xml2', 'purrr'), contriburl=)"