Getting Started - OmicSoft Suite V11 and Below
From Array Suite Wiki
Install OmicSoft Studio
Install OmicSoft Studio on Windows
Install OmicSoft Studio on MacOS
Activate OmicSoft Studio
This section contains information relevant to the OmicSoft Studio end-users: How to activate your OmicSoft Studio.
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
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)
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.
Install OmicSoft Server on Ubuntu 20 with mono 6
Start Running ArrayServer
- For first time admin, you can use Typical way to update/restart ArrayServer. Basically, it uses mono-sgen to run
- For advanced admin, server can be maintained using crontab and shell script such as Run-omicsoft.sh
Once the ArrayServer is ready and running, each user can connect to ArrayServer using the server tab in their ArrayStudio client:
Test Your Installation
Please watch the video tutorial for server analysis basics and test the ArrayServer connectivity.
Below are Help pages for additional steps you might need to take once you've finished setting up OmicSoft Suite:
Setting up R engine
Updating OmicSoft Server
Registering Users and User Groups
- Getting Started With Server Analysis
- Running Array Server in Windows
- Master Server and Analytic Server
- Get started with Oshell
- Hardware and Software Requirements for ArrayServer