®

Bionano Access
Installation Guide

Document Number: 30170

Document Revision: AA

For Research Use Only. Not for use in diagnostic procedures.

Copyright © 2020 Bionano Genomics, Inc. All Rights Reserved.
For Research Use Only.
Not for use in diagnostic procedures.

Table of Contents
Introduction .......................................................................................................... 4
Compatibility ......................................................................................................... 4
System Requirements .............................................................................................. 4
Access Updates ..................................................................................................... 4
Prerequisites......................................................................................................... 5
Windows Installation ................................................................................................ 7
Linux Installation .................................................................................................... 8
Macintosh Installation .............................................................................................. 8
Configuration ........................................................................................................ 9
Starting the Web Server........................................................................................... 10
Firewall .............................................................................................................. 11
User Accounts ...................................................................................................... 12
IrysView Customers ............................................................................................... 12
Technical Assistance .............................................................................................. 13

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For Research Use Only.
Not for use in diagnostic procedures.

Legal Notice

For Research Use Only. Not for use in diagnostic procedures.

This material is protected by United States Copyright Law and International Treaties. Unauthorized use of this
material is prohibited. No part of the publication may be copied, reproduced, distributed, translated, reverse-
engineered or transmitted in any form or by any media, or by any means, whether now known or unknown,
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translating into another language or format. The technical data contained herein is intended for ultimate
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latest information available at the time of release. Due to continuous efforts to improve the product, technical
changes may occur that are not reflected in this document. Bionano Genomics reserves the right to make
changes in specifications and other information contained in this publication at any time and without prior notice.
Please contact Bionano Genomics Customer Support for the latest information.

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Bionano Genomics®, Irys®, IrysView®, IrysChip®, IrysPrep®, IrysSolve®, Saphyr®, Saphyr Chip®, Bionano Access®,
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© Copyright 2020 Bionano Genomics, Inc. All rights reserved.

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For Research Use Only.
Not for use in diagnostic procedures.

Introduction
The purpose of this document is to detail how to install and configure Bionano Access®. This document will cover
a variety of approaches for installation. It will cover multiple configurations including shared web server and
standalone installations. It will also cover installation procedures for various operating systems including Linux,
Mac, and Windows. The first part of this document will cover the process for a first time installation. The document
also outlines some considerations specific to existing IrysView® customers.

If you will be integrating this web server with any compute servers, Bionano Tools should be installed on the
compute servers first. To complete the configuration of Bionano Access you will need the static IP address of
compute system which is used to submit computation jobs.

A single shared instance of Bionano Access per organization is the recommended installation. It is not
recommended to install Bionano Access on each user workstation or for each instrument. This would defeat the
collaborative design of Bionano Access. It is possible to run Bionano Access on a workstation in standalone mode
if you do not have a Saphyr instrument or compute servers to visualize Bionano data.

Compatibility
Bionano Access is compatible with data generated by a Saphyr® instrument and bioinformatics output from the
Bionano Solve pipeline. Bionano Access has also been tested for compatibility with existing Irys data generated
by Auto Detect 2.1.4 and IrysSolve 2.1 pipeline. Bionano Access can be run on a virtual server if needed. Bionano
Access is currently supported on the following operating systems:

• CentOS 7.x

• RHEL 7.x

• Macintosh (Catalina)

• Windows 10

System Requirements
16 GB of memory for standalone installations and 32 GB for shared web servers is recommended. For disk you
can estimate approximately 5 GB per assembly you plan to retain on the web server. The web server is very
lightweight and will run easily on most systems. If you have a large number of concurrent users or you are
noticing performance issues contact support to help identify a configuration that will work best for your situation.

Access Updates
The prerequisite software packages (see Prerequisites section below) only need to be installed once. To update
your Access, perform the Access installation again (see section Windows Installation or Linux/Macintosh

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Installation). The Bionano Access install can be run as many times as desired. It will not remove or overwrite any
of your data, files, or configurations. You can determine the current version of Bionano Access installed by looking
at the Access Help Page (http://<servername>:3005/Help/HelpIndex.html).

For Windows:

• Stop your Bionano Access web server.

• Go to the control panel, select programs and features.

• Uninstall Nodejs

• Run the installation for Node.js 12.16.1

For Mac:

• Stop your Bionano Access web server

• Run the installation for Node.js 12.16.1

For Linux (Centos / Redhat):

• Stop your Bionano Access web server

• Issue the following commands.

sudo yum remove nodejs

wget --no-check-certificate https://rpm.nodesource.com/pub_8.x/el/7/x86_64/nodejs-8.9.4-
1nodesource.x86_64.rpm -P /home/bionano/
sudo yum install /home/bionano/nodejs-8.9.4-1nodesource.x86_64.rpm

Prerequisites
Bionano Access requires PostgreSQL 9.6, Perl 5, and nodejs 8.9.4 or greater. Links have been provided below to
the appropriate installations instructions based on your operating system. Do not install different versions than
what has been indicated. Be sure to perform these installations with administrator rights. During install, Stack
Builder is not required and use default paths and ports during install.

For Windows:

• Perl 5.24

• PostgreSQL 12 (set password to “1rysview”, use port 5432)

• Node.js 8.9.4 or greater

• Java 1.8

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For Macintosh:

• MacOS Sierra 10.12

• Perl 5.24

• Python 2.7.15 (required by PostgreSQL for Mac)

• PostgreSQL 11 (set password to “1rysview”, use port 5432, and do not install Stack Builder)

• Nodejs 8.9.4

• Java 1.8

For CentOS 7 and RHEL 7:

The commands to install the required prerequisite software on Centos and RedHat have been provided below.

# install perl
sudo yum install –y perl

# install java
sudo yum install java-1.8.0-openjdk

#install nodejs
curl --silent --location https://rpm.nodesource.com/setup_8.x | sudo bash -
sudo yum install –y nodejs

#install postgresql
sudo yum install https://download.postgresql.org/pub/repos/yum/reporpms/EL-7-x86_64/pgdg-redhat-repo-latest.noarch.rpm

sudo yum install postgresql12 postgresql-12-server

sudo yum install postgresql12-contrib
sudo /usr/pgsql-12/bin/postgresql-12-setup initdb
sudo cp /var/lib/pgsql/12/data/pg_hba.conf /var/lib/pgsql/12/data/pg_hba.conf.orig
sudo bash -c 'echo "local all all peer">/var/lib/pgsql/12/data/pg_hba.conf'
sudo bash -c 'echo "host all all 127.0.0.1/32 md5" >>/var/lib/pgsql/12/data/pg_hba.conf'
sudo bash -c 'echo "host all all ::1/128 md5" >>/var/lib/pgsql/12/data/pg_hba.conf'

#start postgresql service

sudo systemctl start postgresql-12
sudo systemctl enable postgresql-12
sudo -i -u postgres psql -U postgres -d postgres -c "alter user postgres with password '1rysview';"
sudo systemctl restart postgresql-12

You will also need to establish rsa keys and keyless login to any servers that will be used for detection or
assembly servers before running the install the first time. To generate new rsa keys use this command as the
bionano user:
ssh-keygen -t rsa

To setup keyless login for the bionano account use this command where <<servername>> is the DNS name for
that server or the IP address. Test it with an ssh connection afterwards. You should not be prompted for a
password if it worked.

ssh-copy-id <<servername>>

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WARNING: Please make sure both PostgreSQL and Java are in your path before attempting the Bionano
Access Install. You can test this by trying the ‘psql’ or ‘java’ commands at a command prompt. If they are not
recognized you need to update your path. Example commands to update your path environment variable have
been provided below, but they may vary depending on your exact system. Please note Mac Catalina OS
requires PATH to be added while in bash.

Mac:

PATH="/Library/PostgreSQL/11/bin:$PATH”

Linux:

export PATH=$PATH:/usr/pgsql-12/bin/

Windows:

• Right click your computer in Windows Explorer and click properties

• Select Advanced system settings

• Click Environment Variables button

• Under system variables (not user variables) select Path

• Click the Edit button

• Add (if not already there) C:\Program Files\PostgreSQL\9.6\bin

• Add (if not already there) C:\Program Files (x86)\Java\jdk1.8.0_161\bin

• Click Ok (x3)

Windows Installation
64 bit Windows 7 or greater is supported. Follow the instructions below to complete a Windows installation.

Installation Steps:
1. Make sure the system has Internet access.

2. Make sure the active account has administrator rights.

3. Download the Bionano Access Windows Setup (Access_Setup.exe) from the Bionano Software
Download page.

4. Right click on the Access_Setup.exe file and select ‘Run as Administrator’.

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For Research Use Only.
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Linux Installation
The majority of our in house testing is performed using CentOS. As such CentOS is the recommended operating
system. However it is known that other organizations often prefer other flavors of Linux. Testing has been
performed using RedHat, Ubuntu, and Darwin (Macintosh). Other versions of Linux are likely to be compatible as
well, but have not been validated for use at this time. The following instructions will guide you how to install
Bionano Access on a Linux system.

If you are not already applying security updates to your system on a regular basis we recommend running ‘yum
update’ on your linux operating system prior to installing the latest version of Bionano Access. This operation
requires Internet access and will update the libraries on your system to the latest versions including various
security updates. Be sure to reboot your system after applying the latest patches when your system is idle.

1. Verify the installation system has internet access.

2. Create a bionano user account that has sudo privileges.

3. Download the Bionano Access Linux/Mac Installation (Access-Install.tar.gz) from the Bionano Software
Downloads page. Be sure to delete previous installation tar files before downloading the latest
installation tar file.

4. Extract the file to /home/bionano:

tar –zxf Access-Install.tar.gz –C /home/bionano

5. Run installation script:

sudo /home/bionano/Access-Install/install.sh

Macintosh Installation
Mac installations are intended for standalone use only. We do not intend for mac systems to function as shared
web servers. You may be prompted for your Mac admin password during the installation. The install script will
install nodejs if it is not already on your system.

1. Verify the installation system has internet access.

2. Download the Bionano Access Linux/Mac Installation (Access-Install.tar.gz) from the Bionano Software
Downloads page to your home directory.

3. Open a terminal window and go to your home directory (cd ~/).

4. Run this command: bash

5. Extract the install file in your home directory (tar –xvf Access-Install.tar.gz)

6. Go into the Access-Install directory (cd ./Access-Install)

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7. Run this command: ./install_mac.sh

8. Enter user password and PostgreSQL password (“1rysview”) accordingly

Configuration
A configuration file is used to specify your Bionano Access setup. This file tells Bionano Access where to find files
and what compute servers it should communicate with. Specify the configuration file by name when you start the
web server. If you plan to run Bionano Access in standalone mode with no instruments or compute servers you do
not have to perform any configuration steps and you can skip the balance of the Configuration section.

Bionano Access can be configured to work with a combination of Saphyr instruments and or compute servers.
You need to create an access.txt file in the …/bionano/access/web/Server/Config folder for your specific
configuration. In the Config folder we provided various template files you can use as a starting point. An
access.txt file is not provided in the installation so that we do not overwrite your configuration during future
updates.

Example access.txt Configuration File

{
"psfDetectServer":"193.168.50.31",
"assemblyServers”:["193.168.50.31"]
"icsShare":"\\\\193.168.50.31\\share",
"webServerShare":"\\\\193.168.50.31\\share",
"irysSolveShare":"/home/bionano/access/share",
"icsShareRelPath":"chips",
"webServerShareJobs":"jobs",
"webServerRelLocalFiles":"",
"webServerPort":"3005",
"solveServerUser":"bionano",
"scriptDir":"/home/bionano/tools/access/1.0",
"refAlignerDir":"tools/pipeline/1.0/REFALIGNER/1.0",
"irysSolveListenIP": "10.10.1.13"
}

Configuration Settings

Adjust the following properties in your access configuration file to establish proper connections with the Saphyr
Instrument Control Software and your compute servers.

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Property Value Example

psfDetectServer This should be the IP address on the Saphyr “193.168.50.31”

Compute Server accessible to the Bionano Access
Web Server. If you have more than one instrument it
would be the primary Saphyr Compute server in
your cluster. This value must be a static IP address.

irysSolveListenIP This should be set to the IP address for the Bionano “10.10.1.13”
Access Web server that is accessible to all the
compute servers. In some cases the web server
may be dual homed so that the compute servers can
be within an isolated VLAN. In this case the web
server may have more than one IP address. The
compute servers will curl http requests to the web
server to update job status using this IP address.
This value must be a static IP address.

icsShare This is the path where the Saphyr Instrument “\\\\193.168.50.31\\share”

Control Software will write images captured from the
instrument for image detection. This path should be
relative to the instrument control PC.

webServerShare This is the path to the share for images from the Windows:
instrument and output for the pipeline. If the web “\\\\193.168.50.31\\share”
server is running on a Windows machine this value
Linux:
should be the same as the icsShare property. If the
“/home/bionano/access/share”
web server is running on a Linux system it should be
the same as the irysSolveShare property.

assemblyServers Input the static IP address of compute node that can [“193.168.50.31”]
take SGE job submissions.

webServerPort The TCP port used by the Access application 3005

Starting the Web Server

First open a command prompt and navigate to the following directory:

(Windows) c:\bionano\access\web\Server

(Linux) /home/bionano/access/web/Server

To start Bionano Access Web Server in standalone mode issue the following command:

node --max-old-space-size=16384 server default

To start Bionano Access Web Server with your access.txt configuration issue this command:

node --max-old-space-size=32768 server access

“node” is the command to start nodejs. The “--max-old-space-size” argument increases the V8 JavaScript engine

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memory use to be optimized for our larger data files. ‘server’ is our starting nodejs file and the final parameter
(access or default) is the configuration file to use.

The web server should then be accessible from a browser using the IP address or DNS name for the webserver
plus the port the server is running on. 3005 is our default port. You can change the port for the web server in the
configuration file by changing the ‘webServerPort’ setting. If you use port 80 you will not need to add a port
number to your URL, but there are known issues with curl responses from the compute servers routing to port 80
on some networks due to security restrictions. If you do not know your Web Server’s IP address or DNS, contact
your IT department for details, and if using standalone mode on a local machine such as a desktop or laptop, use
‘localhost’ in place of an IP address. Other users would require the IP address or DNS name instead of localhost
to access your machine.

Ex. http://192.168.48.57:3005, http://bionano-227:3005/

On CentOS and RedHat if you close your SSH session the server will stop. You can use the following commands
to detach from the process and allow it to continue running after you exit. When you run this command the
console output will be logged to the nohup.out file in the …/bionano/access/web/Server directory.

nohup node --max-old-space-size=32768 server access & disown

Important note:

To start access the web server in Linux, you can only use the “bionano” account and the bionano account must
have sudo privilege. Please do not start the access web server using the root account in Linux.

Firewall
There are a few security considerations with your Bionano Access web server. First if you have firewall security
you will need to allow the following traffic from the Bionano Access web server. Generally if you are running in
standalone these considerations would not apply.

Firewall information:
Source System Target System Protocol
Bionano Access Web Server psfDetectServer SSH port 22
assemblyServers

All compute servers Bionano Access Web Server HTTP

Saphyr Instrument Control PC (port is set as webServerPort in config file)
Workstation Browsers

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User Accounts
When you first access the web server you will be prompted to log in. There is a default user account (below)
provided you can use to access the system. Once you have logged in, create user accounts for your team
members. We recommend that you disable or modify the default account once you have finished creating user
accounts for your organization. Do not use shared accounts between users, that defeats how the notification
scheme is designed to operate and it violates security guidelines for clinical environments. If you change the
default account please notify Bionano Support or provide them an account you want them to use when servicing
your system.

Default Account:
Username: bionanoadmin
Password: admin

IrysView Customers
Customers with an existing Irys instrument will continue to use Auto Detect 2.1.4 for image detection. They will
then import the generated bnx files manually into a project in Bionano Access. The Experiment Design module
and dashboards for real time monitoring in Bionano Access are not compatible with the Irys instrument. Existing
Irys data can be imported into Bionano Access using the import feature. Complex objects such as assemblies and
scaffolds must be tar zipped into a single file in the correct format. Scripts to compress and zip existing Irys data
for upload along with detailed instructions can be found on our AccessImportUtils project on GitHub.

It is recommended that Irys owners install the Bionano Access software on their existing workstation dedicated to
Auto Detect. That system has sufficient computing resources to handle the web server. Existing IrysSolve servers
can be converted to Irys Compute servers running Bionano Solve v3.0, but this process requires Bionano
Technical Support involvement. The system will be reimaged so any data on the system will be erased. Important
data should be archived before the system is re-imaged.

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Technical Assistance
For technical assistance, contact Bionano Genomics Technical Support.

You can retrieve documentation on Bionano products, SDS's, certificates of analysis, frequently asked questions,
and other related documents from the Support website or by request through e-mail and telephone.

Type Contact

Email
support@bionanogenomics.com

Phone
Hours of Operation:

Monday through Friday, 9:00 a.m. to 5:00 p.m., PST

US: +1 (858) 888-7663

Website
www.bionanogenomics.com/support

Bionano Genomics, Inc.

9540 Towne Centre Drive, Suite 100
San Diego, CA 92121