Standalone server (tomcat)

At the moment we support two OS variants.

  • CentOS (6.x)
  • RedHat (6.x)

There are currently two ways of installing MOLGENIS on the server. We use several building blocks to deploy MOLGENIS on servers. The configuration is based upon RPM's which are used in Ansible to configure the deployment.

The architecture of MOLGENIS is displayed in the following figure.

MOLGENIS components

Ansible based installation

See: ansible installation

RPM based installation

To install MOLGENIS you can also run the RPM's on the system.

Add repositories

You need to add the repository to access the RPM's:

Add these files to /etc/yum.repos.d

molgenis.repo

[molgenis]
name=MOLGENIS releases repository
baseurl=https://registry.molgenis.org/repository/yum-releases/
enabled=1
protect=0
gpgcheck=0
metadata_expire=30s
autorefresh=1
type=rpm-md

elasticsearch.repo

[elasticsearch-5.x]
name=Elasticsearch repository for 5.x packages
baseurl=https://artifacts.elastic.co/packages/5.x/yum
gpgcheck=1
gpgkey=https://artifacts.elastic.co/GPG-KEY-elasticsearch
enabled=1
autorefresh=1
type=rpm-md

postgres.repo

[pgdg11]
name=PostgreSQL 11.1 $releasever - $basearch
baseurl=https://download.postgresql.org/pub/repos/yum/11/redhat/rhel-$releasever-$basearch
enabled=1
gpgcheck=0

Then type yum update

Install packages

Then you need to install the following artifacts:

  • tomcat
  • adopt-openjdk
  • minio
  • elasticsearch
  • postgresql11-server
  • molgenis
  • httpd
  • optional opencpu
    • opencpu-server
    • rapache
  • optional python3

You can do this by typing this command: yum install #package name#.

note: the order of the packages is important. We do no have requirements set the right way.

Configure packages

Postgres

You need to bootstrap the database with this snippet in PSQL:

CREATE DATABASE molgenis;
CREATE USER molgenis WITH PASSWORD 'molgenis';
GRANT ALL PRIVILEGES ON SCHEMA molgenis TO molgenis;

In the pg_hba.conf You need to update to these lines:

# TYPE  DATABASE        USER            ADDRESS                 METHOD

# "local" is for Unix domain socket connections only
local   all             all                                     peer
# IPv4 local connections:
host    all             all             127.0.0.1/32            md5
# IPv6 local connections:
host    all             all             ::1/128                 md5
# Allow replication connections from localhost, by a user with the
# replication privilege.
#local   replication     postgres                                peer
#host    replication     postgres        127.0.0.1/32            ident
#host    replication     postgres        ::1/128                 ident

In the postgres.conf you need to update these lines:

max_locks_per_transaction = 1024

Restart the service.

Elasticsearch

Open elasticsearch.yml in the Elasticsearch config directory and set the following properties:

cluster.name: molgenis
node.name: node-1
indices.query.bool.max_clause_count: 131072

In the /etc/security/limits.conf update this line:

elasticsearch  -  nofile  65536

Add this this file in /etc/sysctl.d/99-elasticsearch.conf with the following content.

vm.swappiness=1

Restart the service.

Configure Tomcat

After you install Apache Tomcat you first need to install MOLGENIS before you start the service.

Configure HTTPD

We use proxy passes to expose Tomcat through Apache. You can use this file as template to expose your MOLGENIS instance. Create the file in /etc/httpd/conf.d/

molgenis.conf

<VirtualHost molgenis.your-domain.ext:80>

    ServerAdmin admin@molgenis.your-domain.ext

    ServerName molgenis.your-domain.ext
    ServerAlias molgenis.your-domain.ext

    RewriteEngine on
    RewriteCond %{SERVER_NAME} =molgenis.your-domain.ext
    RewriteRule ^ https://%{SERVER_NAME}%{REQUEST_URI} [NE,R=permanent]

</VirtualHost>

<VirtualHost molgenis.your-domain.ext:443>

    ServerAdmin admin@your-domain.ext

    ServerName molgenis.your-domain.ext
    ServerAlias molgenis.your-domain.ext

    ProxyRequests Off
    ProxyPreserveHost On

    ProxyPass / http://localhost:8080/
    ProxyPassReverse / http://localhost:8080/

    RequestHeader set X-Forwarded-Proto "https"
    RequestHeader set X-Forwarded-Port "443"

    SSLEngine On

    SSLCertificateFile /etc/pki/tls/certs/**#your cert#**.crt
    SSLCertificateKeyFile /etc/pki/tls/private/**#your key#**.key
    SSLCertificateChainFile /etc/pki/tls/certs/**#your server-chain#**.crt

</VirtualHost>

Restart the service.

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