Getting Started - OmicSoft Suite V11 and Below

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Tips.pngThe information on this page is relevant to OmicSoft Suite V11 and below. Please visit Getting Started for updated information on newer versions.



Contents

OmicSoft Studio

Requirements

Tips.png This section contains information relevant to the IT team.

Hardware Requirements

Installation Requirements for OmicSoft Studio

IT Requirements

Array Studio IT Requirements

Install OmicSoft Studio

Tips.png This section contains information relevant to the OmicSoft Studio end-user.


Install OmicSoft Studio on Windows

Install OmicSoft Studio on Windows

Install OmicSoft Studio on MacOS

ArrayStudio ClickOnce Launch in Mac

Activate OmicSoft Studio

This section contains information relevant to the OmicSoft Studio end-users: How to activate your OmicSoft Studio.


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OmicSoft Server

Tips.pngThis section contains information relevant to the OmicSoft Server Administrators.

Prerequisites

For hardware requirements and storage needs, please see Hardware_/_Software_requirements_for_Array_Server. Most of our clients run OmicSoft Server on a Linux machine, which can enable HPC cluster and external tool integration

Installing OmicSoft Server

On Linux

Configure your Linux environment

Open Firewall Ports

The ArrayServer machine will need to allow certain connections to occur from Array Studio.

For example, if the ArrayServer.cfg file is configured to allow connections to

(ArrayServer.cfg)
...
port=8064
port2=8065
port3=8066
DataPortBegin=50801
DataPortEnd=50900
...

(see below for details),

Then firewalld , is installed/enabled, would need to be changed as follows:

firewall-cmd --permanent --add-port=8064-8066/tcp
firewall-cmd --permanent --add-port=50801-50900/tcp
firewall-cmd --reload

Download Array Server Updater

On command line, type
sudo mkdir /opt/arrayserver
sudo cd /opt/arrayserver
sudo wget -c http://omicsoft.com/software_update/OmicsoftUpdater.exe

Download Array Server using the updater

sudo touch ArrayServerLinuxBeta.exe
sudo /opt/mono-6.12/bin/mono ./OmicsoftUpdater.exe

Make sure the /opt folder and it's subfolders are owner by the current user (ubuntu):

sudo chown -R $USER /opt (in order to avoid having to run everything as sudo)

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Download and Update Configuration Files

Download configuration template

cd /opt/arrayserver
wget https://resources.omicsoft.com/software/ArrayServer/ArrayServerConfigTemplate.zip
unzip ArrayServerConfigTemplate.zip


Admin will have to modify three important configuration files based on downloaded template:

  • ArrayServer.cfg is the key configuration file. A few important options are :
    • Port, Port2 and Port3 define the port number for data communication between ArrayStudio client and ArrayServer. Make sure to open these ports on firewall.
    • DataPortBegin and DataPortEnd define the port range for Threaded Ftp data transfer. Make sure to open the port range on firewall.
    • 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 sit 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).
    • The Folder section defines additional local or network folders monitored and available for access by array server users.
    • 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.
  • 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.
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Install OmicSoft Server on Ubuntu 20 with mono 6

Install OmicSoft Server On Ubuntu 20


Start Running ArrayServer

Once the ArrayServer is ready and running, each user can connect to ArrayServer using the server tab in their ArrayStudio client:

ConnectServer.png

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Test Your Installation

Please watch the video tutorial for server analysis basics and test the ArrayServer connectivity.

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Next Steps

Below are Help pages for additional steps you might need to take once you've finished setting up OmicSoft Suite:

Setting up R engine

Install_R_Packages_for_ArrayServer

Updating OmicSoft Server

Typical way to update/restart ArrayServer

Registering Users and User Groups

ManageUsers.pdf

Installing Lands

Land PublishCloudLand.pdf


Related Articles

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