Run OmicSoft Server v12 on Amazon Linux 2 from Pre-built AMIs

From Array Suite Wiki
Tips.pngThis page describes the installation steps for OmicSoft Server with OmicSoft Suite v12.1, released mid-May 2022. If you're using OmicSoft Suite v11.7 or earlier, please visit Getting Started - OmicSoft Suite V11 and Below.

Create the EC2 instance

The AMIs were built for use with OmicSoft Suite 12, by following the steps described on Install OmicSoft Server v12 on Amazon Linux 2.

  • Create a new EC2 instance by choosing the appropriate AMI for your AWS region and following the hardware requirements described at Hardware/Software Requirements for OmicSoft Server.
  • Connect to your instance via SSH using the ec2-user user.
    • Make sure you are using the private key corresponding to the "key pair" specified when starting up the EC2 instance.
Date Created Region AMI Name AMI ID AMI Snapshot ID
25-05-2022 US-East-1 (Virginia) OmicsoftServer.V12.1-ue1-p-mono6-amazonlinux2-20220520 ami-043311cb8ac2e44cb snap-000a660e8a1b04532
25-05-2022 US-East-2 (Ohio) OmicsoftServer.V12-ue2-p-mono6-amazonlinux2-20220520 ami-0071b0941c6e633a0 snap-0b91313382398127e
25-05-2022 US-West-1 (N. California) OmicsoftServer.V12.1-ue1-p-mono6-amazonlinux2-20220520 ami-0794b1f28aeb8cbe0 snap-0a233c2ac1a0a197f
25-05-2022 US-West-2 (Oregon) OmicsoftServer.V12.1-ue1-p-mono6-amazonlinux2-20220520 ami-026f85d47e8bccf6a snap-0dcfb46a4068a7a80
25-05-2022 EU-West-1 (Ireland) OmicsoftServer.V12.1-ue1-p-mono6-amazonlinux2-20220520 ami-04e0baa746ad483c7 snap-069abd40a0da833d9
25-05-2022 EU-West-2 (London) OmicsoftServer.V12.1-ue1-p-mono6-amazonlinux2-20220520 ami-0e41f551a7ef84740 snap-0115dcea1bc9689a5
25-05-2022 EU-Central-1 (Frankfurt) OmicsoftServer.V12.1-ue1-p-mono6-amazonlinux2-20220520 ami-02677e603036b9a0b snap-021eb9d60a84ad15f
25-05-2022 AP-Northeast-1 (Tokyo) OmicsoftServer.V12.1-ue1-p-mono6-amazonlinux2-20220520 ami-0e820690a9b3415e8 snap-02059e08486d12b38
25-05-2022 AP-Southeast-2 (Sydney) OmicsoftServer.V12.1-ue1-p-mono6-amazonlinux2-20220520 ami-0f51111ecb807c90c snap-0b50bb68da01ffb89

Set up OmicSoft Applications

Update OmicSoft Server

Run Omicsoft Service Updater

If the mono process instance running the Omicsoft Server is started, make sure it is stopped first.

$ cd /opt/arrayserver

# If not downloaded recently, get the latest version of OmicSoftServiceUpdater: wget -c
$ mono ./OmicsoftServiceUpdater.exe

Update ArrayServer.cfg

The downloaded template contains the ArrayServer.cfg, which is the key configuration file. The following sections and fields are mandatory:

  • License section - server license code for your company
  • Port2 and Port3 - define the port number for data communication (gRPC and SFTP data transfer) between OmicSoft Studio client and OmicSoft Server. Make sure to open these ports on firewall.
  • CertificateThumbprint - specifies the server certificate thumbprint
  • MasterServerUrl - identify the DNS name and the gRPC port on which the server can be accessed
  • OmicSoft directories
    • BaseDirectory - this will be the working directory of the array server, storing all the raw and possessed data. Depending on the projects, it can take huge amount of disk space.
    • OmicsoftDirectory - This directory can be defined locally or on a network drive. All the reference genomes, gene models, Affymetrix CDF files, log files, etc. are stored in this folder.
    • TempDirectory - This should be a local directory (i.e. NOT a network drive) for fast read and write access. It can take twice the size of an unzipped fastq file in some NGS tasks (we would suggest use a drive with at least 100GB storage).
    • LandDirectory - directory for Land data storage. Depending on the number of Lands installed, this can take several hundred GB.
  • Locations of Mono 6 binaries installed on your Oshell instance(s), which are required by jobs started through the server:
  • The [Folder] section defines additional local or network folders monitored and available for access by array server users.

To enable cloud-based NGS analysis with the Array Server Cloud add-on, please follow the instructions from ArrayServer_Configuration_with_Cloud. The following properties must be configured within ArrayServer.cfg.

For a full list of options, see ArrayServer.cfg for more details. For master-analytic server setup, please read Master Server and Analytic Server for more details.

Update metadata template files

  • default.template: it defines project level meta data, such as requiring project title, and list organism. Admin can customize the project meta data based on this template file and even enforce controlled vocabulary. For first time setup, the default values we prepared should be good to go. Admin can further customized based on the understanding of default.template wiki article.
  • sample.template: it defines sample level meta data, such as requiring users to fill organism and tissue for each samples in sample registration. Admin can customize the sample meta based on this template file and even enforce controlled vocabulary. For first time setup, the default values we prepared should be good to go. Admin can further customize based on the understanding of sample.template wiki article.

Update Oshell

$ cd /opt/oshell
# If not downloaded recently, get the latest version of OmicSoftServiceUpdater: wget -c
$ mono ./OmicSoftServiceUpdater.exe
$ mono ./oshell.exe --version
OShell version=12.1.X.X

Configure Certificates


  • DNS name
    • DNS must point to the OmicSoft Server machine (ex.:
    • DNS must be reachable from all machines where OmicSoft Studio/Land Explorer/Oshell and (if applicable) Analytic servers will be installed
    • DNS name must point to a static/fixed IP
    • DNS must have a valid TLS >= 1.2 signed server certificate (including the associated private key)

Make sure that the server is reachable using the DNS name, both from outside the server network, but also from the server machine itself:

Pinging [X.XXX.XX.XX] with 32 bytes of data:
Reply from X.XXX.XX.XX: bytes=32 time=230ms TTL=37
Ping statistics for
   Packets: Sent = 4, Received = 4, Lost = 0 (0% loss),
Approximate round trip times in milli-seconds:
   Minimum = 230ms, Maximum = 231ms, Average = 230ms
  • TLS certificate
    • The certificate must be signed by a public certificate authority (no self-signed certificates can be used).
    • The certificate should be in .pfx (PKCS #12) format, containing the entire certificate chain and the private key.
    • You also need the intermediate CA certificates in separate files, so you can import them in the Mono store.

Information on how to obtain all the required files can be found Certificates Setup page.

Certificates Setup

Set up the TLS Certificate for Server

If you don't have all the required files, please review the Certificates Setup page.

Install the intermediate CA certificate(s)

Intermediate CA can be in the following formats: .PEM, .CRT, .CER.

Import the intermediate CA certificates:

  • the current user intermediate CA store
$ certmgr -add -c -v CA IntermediateCA1.cer
  • the machine intermediate CA store
$ sudo certmgr -add -c -v -m CA IntermediateCA1.cer

Verify certificates installation with:

$ certmgr -list -c CA
$ sudo /opt/mono-6.12.0/bin/certmgr -list -c -m CA
Install the server certificate(s)

Import the server certificate in the machine-level ( -m param. ), personal ('My') store, from the PFX file (that must have also the private key included). The private key password might be needed for this step:

$ sudo certmgr -add -c -v -p privatekeypassword -m My cert.pfx

Verify if the certificate was properly imported with:

$ sudo certmgr -list -c -m My

Update Omicsoft server configuration file

Get the server certificate thumbprint that must be set in ArrayServer.cfg using the PFX file:

$ openssl pkcs12 -in cert.pfx -nodes -passin pass:privatekeypassword | openssl x509 -noout -fingerprint | cut -f2 -d'='

Set/Update the thumbprint in ArrayServer.cfg


Start OmicSoft Server

$ cd /opt/arrayserver/
$ mono ./OmicSoftServer.exe >> ./run.log &
$ & disown -h