OmicSoft Suite IT Requirements

From Array Suite Wiki

Jump to: navigation, search
Tips.png The information below is valid for OmicSoft Suite v12 or newer


Contents

Overview

OmicSoft Suite (OmicSoft Studio + OmicSoft Server) integrates with a number of internal and external network resources, so some internet connectivity is required. This page describes the most common requirements that an Information Technology (IT) department may have to accommodate. Some companies may have site-level (or even department-level) IT, as well as corporate IT, so it can take initial effort to enable the required connections. OmicSoft Support is always happy to talk to IT groups to help them understand the required connections.

  • OmicSoft Studio requires a connection to the internet, and may be improperly flagged anti-malware software. Talk with your IT team about any software that might block OmicSoft Studio.
  • OmicSoft Studio will often require a change to Firewall settings to allow limited connections. Work with your IT team to implement these changes efficiently, and OmicSoft support can help with configuration to find settings that are compatible with IT policies.
  • OmicSoft Studio usually connects to either a dedicated OmicSoft Server instance or a QIAGEN hosted OmicSoft Server. If you have a dedicated OmicSoft Server instance, work with your IT team to find out the appropriate OmicSoft Server domain name and ports. If you connect to a QIAGEN hosted server, check your welcome e-mail for login info and connections.

OmicSoft Suite computer requirements


OmicSoft Suite Firewall Permissions

In order for OmicSoft Studio and OmicSoft Server to function properly, certain internet connections must be allowed (All file type extensions should be allowed from these locations:

   oslicensing-iad.omicsoft.com:443 (OmicSoft primary license activation server)
   oslicensing-eu.omicsoft.com:443 (OmicSoft backup license activation server)
   dataservice-iad.omicsoft.com:443 (OmicSoft data services - genome browser, gene autofill, bas server)
   https://resources.omicsoft.com/* (downloading software, reference libraries, and datasets from OmicSoft)
   https://analysis.ingenuity.com/* (IPA analysis)

HTTP(S) connections

The following external resource URLs should be open (hopefully these are already opened)

   https://www.ncbi.nlm.nih.gov/*
   https://ftp.ncbi.nih.gov/*
   https://eutils.ncbi.nlm.nih.gov/*
   https://www.affymetrix.com/*
   https://portal.genego.com/*
   https://decipher.sanger.ac.uk/*
   https://secondslide.com/*
   https://portal.biobase-international.com/*
   https://dcc.icgc.org/*
   https://eutils.ncbi.nlm.nih.gov/*
   https://tcga-data.nci.nih.gov/*
   https://tcga-data-secure.nci.nih.gov/*
   https://confluence.broadinstitute.org/*
   http://tcga-data.nci.nih.gov/*
   http://genome.ucsc.edu/*
   http://www.hapmap.org/*
   http://www.genecards.org/*
   http://pubs.broadinstitute.org/*
   http://www.regulomedb.org/*
   http://www.ensembl.org/*
   http://www.broadinstitute.org/*
   http://dcc.icgc.org/*
   http://services.ichip.de/*
   http://www.encodeproject.org/*
   http://omim.org/*
   http://www.genenames.org/*
   http://www.uniprot.org/*
   http://cancer.sanger.ac.uk/*
   http://www.ebi.ac.uk/*
   http://www.affymetrix.com/*
   http://microrna.sanger.ac.uk/*
   http://srs.ebi.ac.uk/*
   http://amigo.geneontology.org/*
   http://projects.tcag.ca/*
   http://eutils.ncbi.nlm.nih.gov/*

FTP connections

For details on why and how FTP connections are used please check FTP connections in v12. The following external resource URLs should be open for FTP downloads.

   ftp://ftp.icgc.oicr.on.ca/*
   ftp://ftp.ebi.ac.uk/*
   ftp://ftp.ncbi.nlm.nih.gov/*
   ftp://ftp.ncbi.nih.gov/*
   ftp://ftp-trace.ncbi.nlm.nih.gov/*
   ftp://ftp.sra.ebi.ac.uk/*

Amazon Web Services connections

If you subscribed to an OmicSoft Land product as part of your OmicSoft Server installation, to enable retrieval of the latest Land data the following connections to AWS should be allowed:

   https://*.amazon.com
   https://*.amazonaws.com

If you have configured Omicsoft Suite to use Cloud (http://www.arrayserver.com/wiki/index.php?title=ArrayServer_Configuration_with_Cloud) the following connections to AWS should be allowed both for OmicSoft Server and OmicSoft Studio installations:

   https://*.amazon.com
   https://*.amazonaws.com

If you need more fine grained connection management to AWS S3 resources you would need to find the IP addresses corresponding to the buckets you have mapped as part of your mapped "Cloud Folders".

You could use the following link https://aws.amazon.com/premiumsupport/knowledge-center/s3-find-ip-address-ranges/ for determining the IPs.


To test your connection, you can use telnet to confirm firewall configuration from the command line:

   US Eastern: telnet s3.us-east-1.amazonaws.com 443
   US Western: telnet s3.us-west-2.amazonaws.com 443
   Asia/Oceania: telnet s3.ap-northeast-1.amazonaws.com 443
   Europe/Middle East: telnet s3.eu-central-1.amazonaws.com 443

OmicSoft Studio/OmicSoft Server network Connections

Most OmicSoft Studio users will work in context of an OmicSoft Server connection.

OmicSoft Studio generally requires 2 main connections to OmicSoft Server: gRPC and SFTP.

The ports used by OmicSoft Server can be configured to accommodate your company's IT infrastructure. The default ports are 8065 (gRPC) and 8066 (SFTP).

The same AWS connections mentioned above need to be opened if you work with Cloud (AWS) data. Example questions for IT:

  • "What anti-malware software is on my computer? How can we add exceptions for OmicSoft Studio, including connectivity to required internet resources for the software (listed above)?"
  • "Will OmicSoft Studio be able to navigate through our corporate firewall to reach limited internet resources (listed above)?"
  • "To connect to an (onsite or off-site) OmicSoft Server, what communication ports are allowed?"

Network issues that can prevent OmicSoft Studio function

  • Because of OmicSoft Studio's network connections, it will sometimes be flagged by anti-malware software such as Symantec Antivirus or Trusteer Apex. Please check with your IT department to understand all security software on your computer, and how to allow exceptions for OmicSoft Studio to work properly.
  • If OmicSoft Studio will not start, it is often because one of the required files has been quarantined, so the network IT team will need to whitelist the application.
  • If OmicSoft Studio will start, but connecting to OmicSoft Server gives a message "A socket operation encountered a dead network", check client-side anti-malware (e.g. Trusteer Apex) for indications that it blocked an outgoing communication.
  • License-checking issues often indicate improper proxy configuration. Check with your IT team for the exact parameters of allowed gRPC and SFTP traffic, and proxy setup; this information will be essential for OmicSoft support to diagnose connection issues.