Contents

Agilent SureCall 4.2.1 Sequencer Installation Guide PDF

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Summary of Content for Agilent SureCall 4.2.1 Sequencer Installation Guide PDF

Agilent SureCall 4.2.1

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

Agilent Technologies

Notices Agilent Technologies, Inc. 2020-2021

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Manual Part Number G4890-90007

Edition Revision B0, May 2021

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2 Agilent SureCall Installation Guide

In This Guide

Agilent SureCall Installation Guide

This Installation Guide provides instructions for installing SureCall 4.2.1.

1

Installation of SureCall 4.2.1 for Windows Fresh Install Instructions

This chapter provides instructions for new SureCall users on how to install and get started using SureCall 4.2.1 on computers running the Windows operating system.

2

Installation of SureCall 4.2.1 for Windows Software Upgrade Instructions

This chapter provides instructions for users of SureCall 4.1.2 or 4.2.0 who want to upgrade to SureCall 4.2.1 while retaining all records currently in their SureCall database. It also contains instructions on uninstalling SureCall. The instructions in this chapter are specific for Windows computers.

3

Installation of SureCall 4.2.1 for Macintosh Fresh Install Instructions

This chapter shows you how to install and get started using SureCall 4.2.1 on computers running the macOS Catalina operating system.

4

Installation of Sequence Alignment Tools

This chapter shows you how to install the sequence alignment tools provided by Agilent for use with SureCall 4.2.1.

3

4

Agilent SureCall Installation Guide

1 Installation of SureCall 4.2.1 for Windows Fresh Install Instructions 7

Avoiding common installation issues 8

Preparing for installation 10

Download the software and release notes 10

Check system requirements before you start 11

Set up permissions for installer and users 11

Adjust user account settings 12

Installing a standalone version of SureCall 4.2.1 Windows 13

Installing SureCall 4.2.1 client on additional computers Windows 29

Opening the SureCall 4.2.1 client software 32

Adding users and assign roles 34

Adding a SureDesign user name and password 36

Checking the data download 37

Downloading Software Updates 38

2 Installation of SureCall 4.2.1 for Windows Software Upgrade Instructions 39

Upgrading a standalone version of SureCall 40

Upgrading SureCall on client computers 57

Uninstalling SureCall 65

Uninstall the client and server software for SureCall 65

Uninstall the SureCall client software only 67

3 Installation of SureCall 4.2.1 for Macintosh Fresh Install Instructions 71

Installing Java Standard Edition 11 (Java SE 11) 72

To check which versions of Java are installed 72

To install Java SE 11 73

Preparing for installation 74

Download the software and release notes 74

Agilent SureCall Installation Guide 5

Check system requirements before you start 75

Set up permissions for installer and users 75

Installing a standalone version of SureCall 4.2.1 Macintosh 76

Opening the SureCall 4.2.1 client software 92

Adding a SureDesign user name and password 94

Checking the data download 95

4 Installation of Sequence Alignment Tools 97

Installing Sequence Alignment Tools (GenAligners) 98

Step 1. Uninstall the previous version of GenAligners (if applicable) 98

Step 2. Download the GenAligners installer from the Agilent website 98

Step 3. Install the alignment tools on your computer 99

6 Agilent SureCall Installation Guide

1 Installation of SureCall 4.2.1 for Windows Fresh Install Instructions

Avoiding common installation issues 8

Preparing for installation 10

Installing a standalone version of SureCall 4.2.1 Windows 13

Installing SureCall 4.2.1 client on additional computers Windows 29

Opening the SureCall 4.2.1 client software 32

Adding users and assign roles 34

Adding a SureDesign user name and password 36

Checking the data download 37

Downloading Software Updates 38

This chapter provides instructions for new SureCall users on how to install and get started using SureCall 4.2.1 on computers running the Windows operating system.

For instructions on upgrading from a previous version of SureCall to SureCall 4.2.1, see Chapter 2, Installation of SureCall 4.2.1 for Windows Software Upgrade Instructions on page 39.

For instructions on installing SureCall 4.2.1 on a Macintosh computer, see Chapter 3, Installation of SureCall 4.2.1 for Macintosh Fresh Install Instructions on page 71.

Agilent Technologies

1 Installation of SureCall 4.2.1 for Windows Fresh Install Instructions Avoiding common installation issues

Avoiding common installation issues

8

Before you install the SureCall 4.2.1 software, review Table 1 for a list of common installation issues and how to avoid or resolve them.

Table 1 Common installation issues

Issue How to avoid and/or resolve

The software fails to install or run

properly due to user account

privileges

The user account used to install the software needs to have read/write privileges for

the SureCall installation folder (C:\agilent\SureCallx). Make sure that the user account

used to install the SureCall software has administrator permissions on the system.

Contact your local network administrator to grant read/write permissions to the

installation drive.

The software installation aborts

when the installer detects that the

PC fails to meet minimum

requirements

System requirements must be met for the software to work properly. Review the

requirements in Table 2 on page 11.

At the completion of installation,

SureCall fails to download the

reference and annotation data files

due to incorrect file path specified

as the annotation source

During installation, the SureCall installation wizard allows you to specify a local drive

as the location of the reference and annotation data files that need to be imported into

SureCall (refer to Figure 9 on page 21). If no local file path is entered, then SureCall

downloads those files directly from the Agilent cloud at the completion of the SureCall

installation. This option for entering the file path of a local drive is intended only for

users who have all of the necessary files stored on a local drive (e.g., an externally

connected USB disk).

If you enter a file path for a directory that does not already contain all of the files, then

SureCall will be unable to successfully import the files from that directory into the

software. If you already installed SureCall with the incorrect file source entered, go to

the Admin > Annotation Download screen of the software and click Use Agilent Cloud

to set the source location. Then, click Start Download.

At the completion of installation,

SureCall fails to download the

reference and annotation data files

due to incorrect entry of proxy

settings

During installation, the SureCall installation wizard prompts you to configure the

settings for the proxy server used by your institution (refer to Figure 8 on page 20). Not

all institutions requires users to connect to the internet through a proxy server, in

which case you would leave the settings blank. If you institution does use a proxy

server, contact your local network administrator to obtain the necessary information.

If you already installed SureCall with the incorrect proxy settings, you can edit the

settings from the Admin > SureCall Connector > Proxy screen. Once those settings are

corrected, retry the download of the annotation files from the Admin > Annotation

Download screen (click Start Download to initiate).

Agilent SureCall Installation Guide

Installation of SureCall 4.2.1 for Windows Fresh Install Instructions 1 Avoiding common installation issues

SureCall cannot access the

CommonStorage folder due to lack

of read/write privileges

The CommonStorage folder which SureCall uses for storing workflow output files,

design files, and others must be shared with everyone in the network. The

CommonStorage folder also needs to be accessible to all SureCall client PCs that point

to the SureCall server for storing data. The CommonStorage folder is a subfolder within

the SureCall Server folder (C:\agilent\Agilent_SureCall_4.x\Server\CommonStorage).

The steps for changing the permissions assigned to a folder vary depending on your

operating system. Follow the steps appropriate for your system to share the

CommonStorage folder with everyone on the network.

SureCall does not recognize a user

account

Each SureCall user needs to be given a SureCall account, which can be set up during

installation or after installation is complete. During installation, the SureCall

installation wizard allows you to add SureCall users and configure their roles (refer to

Figure 6 on page 18 and Figure 7 on page 19). If you already installed SureCall, users

with an Administrator role can add accounts from the Admin > User Accounts screen.

The password for a users SureCall account is the same as that users Windows

password.

SureCall workflows using FASTQ

files fail due to absence of the

GenAligners software package

In addition to the SureCall software, you also need to install the sequence alignment

tools if you plan to use SureCall to analyze FASTQ files. Refer to Chapter 4, Installation

of Sequence Alignment Tools on page 7 for instructions.

Table 1 Common installation issues

Issue How to avoid and/or resolve

Agilent SureCall Ins

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1 Installation of SureCall 4.2.1 for Windows Fresh Install Instructions Preparing for installation

Preparing for installation

Download the software and release notes

10

1 Go to www.agilent.com/en/download- software- surecall.

2 Click Download Software.

3 Click the Download link for the Windows version of the software.

4 Select Save File to save the installer on your computer. (This file is a large file. Depending on your internet connection speed, the download can take a long time.)

5 Browse to a location where you want to save the installer program, and then click Save. (Do not start the installation at this time.)

6 Return to www.agilent.com/en/download- software- surecall and click Download Software again.

7 Click the Download link for the Release Notes.

8 Click Save As.

9 Browse to a location where you want to save the release notes.

10 Click Save.

You will also need to download the installer for the sequence alignment tools from the

NOTE www.agilent.com/en/download-software-surecall website. See Installing Sequence

Alignment Tools (GenAligners) on page 98 for instructions.

Agilent SureCall Installation Guide

Installation of SureCall 4.2.1 for Windows Fresh Install Instructions 1 Preparing for installation

Check system requirements before you start

Agilent SureCall Ins

Check to make sure that your computer systems meet the following requirements. All client installations point to the computer on which the server software is installed. See Table 2 for minimum and recommended requirements.

Set up permissions for installer and users

Table 2 System requirements for running SureCall 4.2.1 on Windows computers

Operating system Windows 10 Enterprise, Windows 10 Professional, or Windows Server 2019

Note: For all of these operating systems, the regional setting must be set to English.

Programs Any program that enables you to open PDF files (for example, Adobe Reader)

Processor Minimum: > 2 GHz, 4-core

Recommended: > 3 GHz, 8-core

Working memory (RAM) Without aligners installed: 8 GB

With aligners installed: 12 GB (16 GB recommended)

With aligners installed and running OneSeq analyses: 16 GB (32 GB recommended)

Hard disk space 500 GB (50 GB for genome reference data and annotation data and 450 GB for your

sequencing data)

Display Resolution 1280 x 768 or higher

Make sure that the user account used to install the SureCall 4.2.1 software has administrator permissions on the installation computer.

Make sure that every user account running the SureCall 4.2.1 software has read/write permissions to the following:

The computer where the client software is installed

The installation folder on the computer where the database server is installed

The folders where input data for analyses (e.g., FASTQ and BAM files) will be stored

The folder where output data (e.g., reports) will be stored

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1 Installation of SureCall 4.2.1 for Windows Fresh Install Instructions Preparing for installation

12

The way you set permissions varies between operating systems. Contact your network administrator for help in checking or changing user account permissions. If the correct user account permissions are not set correctly, the software will fail to install or run properly.

Adjust user account settings

Change the User Account Control settings from the default setting to Never Notify.

1 Go to Control Panel.

2 Click User Accounts.

3 Click Change User Account Control setting.

4 Change the setting to Never Notify and click OK.

5 Restart the computer.

Agilent SureCall Installation Guide

Installation of SureCall 4.2.1 for Windows Fresh Install Instructions 1 Installing a standalone version of SureCall 4.2.1 Windows

Installing a standalone version of SureCall 4.2.1 Windows

Agilent SureCall Ins

SureCall consists of two parts: a PostgreSQL database server and the client software. This section includes detailed instructions and important notes for installing SureCall 4.2.1 as a standalone program (i.e. the SureCall client software and server software are on a single computer).

Once you have installed a standalone version of SureCall on one computer, you can install additional copies of the client software on client computers that have network access to the database computer. See Installing SureCall 4.2.1 client on additional computers Windows on page 29.

Only one copy of the server software is installed, and the server software cannot be

NOTE installed without also installing the client software on the same machine. The client is the

program you run when you want to use SureCall. To run the client software, the database

server must be installed. You can run the client software on the same computer as the

server, or from any other computer with the client software installed. After installation, the

server software runs silently in the background and manages the shared database for all

SureCall 4.2.1 users. All client computers must have network access to the server computer

and users must have read/write permissions.

1 Log on to the computer where you want to install a standalone version of SureCall 4.2.1. Use an account that has administrator permissions.

2 Locate the installation program you downloaded in Download the software and release notes on page 10. Double- click the Agilent SureCall 4.2.1.X.exe file to start the installation wizard.

The following message is displayed.

Figure 1 InstallAnywhere dialog box preparing to install

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The installation wizard starts.

Figure 2 Introduction screen for the installation wizard Windows

3 Read the introductory information. Pay particular attention to the information on RAM and hard disk space requirements.

4 Click Next.

The installation wizard performs a check to confirm that your system meets the minimum hardware and operating system requirements. This check may take several minutes. You can review the system requirements in Table 2 on page 11.

If your system does not meet all requirements, installation cannot proceed. In such cases, a message box opens notifying you of the unmet requirements. (The exception is the requirement regarding display resolution, which is not considered critical. The installation wizard permits you to continue installation even if your display resolution does not meet the stated minimum.)

If your system meets all requirements, the wizard proceeds to the License Agreement screen.

Agilent SureCall Installation Guide

Installation of SureCall 4.2.1 for Windows Fresh Install Instructions 1 Installing a standalone version of SureCall 4.2.1 Windows

Agilent SureCall Ins

Figure 3 License Agreement screen Windows

5 Read the license agreement. Select I accept the terms of the License Agreement and then click Next. (Click Previous to review information in a previous section.)

The Choose Install Set screen opens.

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1 Installation of SureCall 4.2.1 for Windows Fresh Install Instructions Installing a standalone version of SureCall 4.2.1 Windows

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Figure 4 Choose Install Set screen Windows

6 Click the icon next to Standalone to install both the database server and client software on this computer.

7 Click Next.

The Enter Administrator Details screen opens.

Agilent SureCall Installation Guide

Installation of SureCall 4.2.1 for Windows Fresh Install Instructions 1 Installing a standalone version of SureCall 4.2.1 Windows

Agilent SureCall Ins

Figure 5 Enter Administrator Details screen Windows

8 The domain and user name of the person currently logged on to the computer appear in the User Account field. If this account is not the administrator for the SureCall 4.2.1 software, type the correct user, using the one of the formats shown below.

For domain user: DOMAIN\username

For local machine: MACHINENAME\username

9 To set up additional SureCall users, mark the check box labeled Add SureCall Users?. In the Password field that appears, type the password for the SureCall administrator account.

If you do not want to set up new users at this time, proceed directly to step 15 on page 19. Note that administrators can set up new users from within SureCall once installation is complete (see Adding users and assign roles on page 34).

10 Click Next.

The Add SureCall Users screen opens.

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1 Installation of SureCall 4.2.1 for Windows Fresh Install Instructions Installing a standalone version of SureCall 4.2.1 Windows

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Figure 6 Add SureCall Users screen Windows

11 The Add SureCall Users screen lists all of the users in the domain or on the local computer. Mark the check box next to the users that you want to add to SureCall.

To search for a user, type the user name into the search box at the top of the screen.

12 Click Next.

13 The Add SureCall Users screen advances to the step for configuring user roles.

Agilent SureCall Installation Guide

Installation of SureCall 4.2.1 for Windows Fresh Install Instructions 1 Installing a standalone version of SureCall 4.2.1 Windows

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Figure 7 Add SureCall Users screen Configure roles step Windows

14 For each user listed on the screen, select a role in the Roles drop- down list.

The options are Administrator, Scientist, and Technician. See the SureCall help system for a description of each role.

15 Click Next.

The Configure Proxy Settings screen opens.

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1 Installation of SureCall 4.2.1 for Windows Fresh Install Instructions Installing a standalone version of SureCall 4.2.1 Windows

20

Figure 8 Configure Proxy Settings screen Windows

16 If your institution requires you to connect to the internet through a proxy server, enter the information for the proxy server in the fields on the Configure Proxy Settings screen. Contact your network administrator to obtain the necessary information.

17 Click Next.

The Data Download Option screen opens.

Agilent SureCall Installation Guide

Installation of SureCall 4.2.1 for Windows Fresh Install Instructions 1 Installing a standalone version of SureCall 4.2.1 Windows

Agilent SureCall Ins

Figure 9 Data Download Option screen Windows

18 Select the default human genome build (hg19 or hg38) to be used as the reference in your analyses.

After installation is complete, the program begins downloading and installing the reference and annotation data for the selected genome build from Agilent Cloud storage.

Once SureCall installation is complete, SureCall administrators can download reference and annotation data for the non- default genome build from the Admin > Annotation Download screen of the software. This screen also has tools for changing the default genome build selection.

19 By default, SureCall will download and install the required reference and annotation data from Agilent Cloud storage immediately after you complete SureCall installation. If you prefer for SureCall to download and install the required data from a local storage folder or a storage folder saved to an external USB drive, enter the file path of that folder in the Provide Data Location field. You can type the file path directly into the field or click Choose to browse to the storage folder.

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1 Installation of SureCall 4.2.1 for Windows Fresh Install Instructions Installing a standalone version of SureCall 4.2.1 Windows

22

Leave the Provide Data Location field blank if you want SureCall to download the required data from Agilent Cloud storage.

If you received an external USB drive from Agilent containing the reference and annotation

NOTE data, plug in the USB drive to your computer and enter the file path of the drive into the

Provide Data Location field.

20 Click Next.

The Choose Install Folder screen opens.

Figure 10 Choose Install Folder screen Windows

21 By default, the program is installed in: C:\agilent\Agilent_SureCall_4.2.1.X (where X is the revision number). If you prefer to install the program in a different location, enter the file path of the desired folder into the provided field. You can type the file path directly into the field or click Choose to browse to the desired folder.

Agilent SureCall Installation Guide

Installation of SureCall 4.2.1 for Windows Fresh Install Instructions 1 Installing a standalone version of SureCall 4.2.1 Windows

Agilent SureCall Ins

If you want to install SureCall in the default location, leave the default file path in the field.

NOTE The installation program folder must not be in the C:\Program Files folder due to

permissions settings in the Windows operating system.

22 Click Next.

The Common Storage Option screen opens.

Figure 11 Common Storage Option screen Windows

23 By default, the common storage files, including the output files for SureCall analyses, are stored in C:\agilent\Agilent_SureCall_4.2.1.X\Server\CommonStorage (where X is the revision number). If you prefer to save the files to a different location, mark the check box labeled Change Common Storage Location. In the field that appears, enter the file path of the desired folder. You

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1 Installation of SureCall 4.2.1 for Windows Fresh Install Instructions Installing a standalone version of SureCall 4.2.1 Windows

24

can type the file path directly into the field or click Choose to browse to the desired folder.

If you want to save the common storage files to the default location, leave the check box unmarked.

24 Click Next.

The Choose Shortcut Folder screen opens.

Figure 12 Choose Shortcut Folder screen Windows

25 By default, program icons are installed in the Agilent SureCall program group on your computer. To select another location for the program icons, select the desired location (on the desktop, for example).

NOTE If more than one user plans to use SureCall 4.2.1 on this computer, select Create Icons for All Users. Otherwise, other users do not see the program icons.

26 Click Next.

Agilent SureCall Installation Guide

Installation of SureCall 4.2.1 for Windows Fresh Install Instructions 1 Installing a standalone version of SureCall 4.2.1 Windows

Agilent SureCall Ins

The Pre- Installation Summary screen opens.

Figure 13 Pre-Installation Summary screen Windows

27 Review the installation setup information. If you want to change any of the settings, click Previous and go back and change the settings. To start the installation, click Install.

The Installing Agilent SureCall screen opens and remains open until the installation is complete.

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Figure 14 Installing Agilent SureCall screen Windows

When the SureCall installation is complete, the Install Complete screen opens.

Agilent SureCall Installation Guide

Installation of SureCall 4.2.1 for Windows Fresh Install Instructions 1 Installing a standalone version of SureCall 4.2.1 Windows

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Figure 15 Install Complete screen Windows

28 Click Done.

The Download window opens and the program begins downloading and installing the reference and annotation data from Agilent Cloud storage (or from the folder you designated in the Data Download Option screen).

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Figure 16 Download screen

During this process, the Download screen remains open and displays which files have been downloaded and installed. Your system needs to be connected to the internet until the process is complete.

29 When the downloads are complete, click Close to close the Download dialog box.

If the download fails or does not complete, you can manually download the missing files from within SureCall. See Checking the data download on page 37.

Agilent SureCall Installation Guide

Installation of SureCall 4.2.1 for Windows Fresh Install Instructions 1 Installing SureCall 4.2.1 client on additional computers Windows

Installing SureCall 4.2.1 client on additional computers Windows

Agilent SureCall Ins

To use other computers to run SureCall 4.2.1 client software (with a shared database), install the client software on each of the computers.

Before installing SureCall 4.2.1 client, install a standalone version of SureCall 4.2.1 on the

NOTE computer that will run the database software. See Installing a standalone version of

SureCall 4.2.1 Windows on page 13.

1 On each computer that you want to run the SureCall 4.2.1 program, run the installation wizard, as described in Installing a standalone version of SureCall 4.2.1 Windows on page 13.

2 When the Choose Install Set screen opens, select Client.

Figure 17 Choose Install Set screen Select Client Windows

3 Click Next.

The Get Server Details screen opens.

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1 Installation of SureCall 4.2.1 for Windows Fresh Install Instructions Installing SureCall 4.2.1 client on additional computers Windows

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Figure 18 Get Server Details screen Windows

4 In the Server Name field, type the assigned computer name or IP address of the computer where you installed the SureCall 4.2.1 database server. (To find the computer name of your current computer, click Start > Control Panel > System.)

5 Accept the default Port, unless your system administrator tells you otherwise.

6 Click Next.

The installer immediately tests the connection to the specified database.

If incorrect database parameters are provided, or the PostgreSQL database service is not

NOTE running, a message is displayed. You can choose to continue the installation and change

database connection parameters when launching the client software. However, Agilent

recommends that you provide the correct database information during installation.

7 Continue the installation wizard. Follow the instructions for the installation wizard to enter administrator information, choose a

Agilent SureCall Installation Guide

Installation of SureCall 4.2.1 for Windows Fresh Install Instructions 1 Installing SureCall 4.2.1 client on additional computers Windows

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shortcut location, and start the installation. For information, see step 8 through step 29 in the section Installing a standalone version of SureCall 4.2.1 Windows on page 13.

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1 Installation of SureCall 4.2.1 for Windows Fresh Install Instructions Opening the SureCall 4.2.1 client software

Opening the SureCall 4.2.1 client software

32

After you install the SureCall database server and client programs as described in this manual, start the program.

1 Double- click the SureCall 4.2.1 icon, or select SureCall 4.2.1 from the Windows Start menu.

How you start the program depends on the choice you made for Shortcut Folder during

NOTE installation.

When the program first opens, the top right panel of the screen displays the login area. The name and domain for the administrator set during installation appear in the fields.

Figure 19 Login area

2 Type your user name and password into the fields. Once logged in, administrators can add additional users and assign their roles.

If you need to change the domain, expand the drop- down list next to Domain and select the correct domain.

3 Click OK.

After you log in for the first time, the following dialog box opens.

Agilent SureCall Installation Guide

Installation of SureCall 4.2.1 for Windows Fresh Install Instructions 1 Opening the SureCall 4.2.1 client software

Agilent SureCall Ins

Figure 20 Enter License dialog box

4 If you do not already have the license file saved to your computer, click Request for license to open the Agilent website to the SureCall license request page. Complete the fields in the request form to obtain a SureCall software license.

The license is contained in a text file.

5 At the bottom of the dialog box, click Browse.

The Open dialog box opens.

6 Browse to the saved license file. Select the file and click Open.

The program loads the content of the file into the text area on the Enter License dialog box.

7 Click OK.

The SureCall program is available for use.

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1 Installation of SureCall 4.2.1 for Windows Fresh Install Instructions Adding users and assign roles

Adding users and assign roles

34

If multiple client users will be connecting to the same SureCall database, the administrator must add the users and assign user roles. The user role determines what capabilities the user has within SureCall. For information on what capabilities each user role has, see the SureCall help system.

1 Go to the User Accounts screen in SureCall.

a At the top of the program window, click Admin.

b On the left side of the screen, click User Accounts.

2 Click Add New User.

The Add New User dialog box opens.

3 If your computer is on a network, add the new user using the following instructions.

a In the Add New User field at the top of the dialog box, type the user name for the new user and click Find. The table in the dialog box lists the users on your network that match the user name you entered.

b Click the row in the table for the user you want to add and click Add User. A message box opens asking you to confirm that you want to add the user.

c Click Yes in the message box. A message box opens confirming that the user was successfully added. Click OK.

4 If your computer is a local machine with no Domain, add the new user using the following instructions.

a In the Add New User field at the top of the dialog box, type the computer name and user in the format machinename\username. (Do not click Find).

b Click Add User. A message box opens asking you to confirm that you want to add the user.

c Click Yes in the message box. A message box opens confirming that the user was successfully added. Click OK.

5 Click Close in the Add New User dialog box to close the dialog box.

The added user is now listed in the table on the User Accounts screen. By default, new users are assigned the role of Technician.

Agilent SureCall Installation Guide

Installation of SureCall 4.2.1 for Windows Fresh Install Instructions 1 Adding users and assign roles

Agilent SureCall Ins

6 If desired, change the role of the new user.

a In the Action column of the table, click Edit.

The Edit User Role dialog box opens.

b In the drop- down list next to Role, select the desired role for the user.

The options are Administrator, Scientist, and Technician. See the SureCall help system for a description of each role.

c Click Save.

The new role is saved and the Edit User Role dialog box closes.

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1 Installation of SureCall 4.2.1 for Windows Fresh Install Instructions Adding a SureDesign user name and password

Adding a SureDesign user name and password

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Before other users can download a design file from SureDesign into SureCall, the administrator must add the SureDesign account information.

1 Go to the SureDesign Settings screen in SureCall.

a At the top of the program window, click Admin.

b On the left side of the screen, click SureCall Connector.

c Click the SureDesign tab near the top of the screen.

2 Type the user name for the SureDesign account into the SureDesign Username field.

In SureDesign, the user name is the e- mail address of the user.

3 In the SureDesign Password field, type the password for the SureDesign account.

4 Click Apply.

5 Click Test Connection.

A message box opens notifying you if the connection test succeeded or failed.

If the connection test passes, you can download design files from SureDesign into SureCall using the tools on the Supporting Files screen.

If the connection test fails, go to the SureDesign website (www.agilent.com/genomics/suredesign) and try logging in. If the login fails, you can reset the password or register for a new account.

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Installation of SureCall 4.2.1 for Windows Fresh Install Instructions 1 Checking the data download

Checking the data download

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When you first installed SureCall, the program automatically downloaded the necessary reference and annotation files from Agilent Cloud storage or from a specified local folder or drive. Downloading the files requires an internet connection and a minimum of 20 GB of disk space.

Before you start running analyses in SureCall, make sure that the program successfully completed the data download process.

1 Go to the Annotation Download screen in SureCall.

a At the top of the program window, click Admin.

b On the left side of the screen, click Annotation Download.

2 Click Refresh Annotation Status.

3 In the message box that opens, click Yes to continue.

The program obtains the status of the data file downloads and displays the statuses in a table on the Annotation Download screen.

4 Check the status of the downloads.

If all files were successfully downloaded. the top right corner of the screen displays the message All data files downloaded successfully.

If some files were not successfully downloaded, click Start Download. The program will connect to the Agilent Cloud storage system, or the local folder or drive specified during SureCall installation, to download the missing files.

The source location for the files is specified on the Admin > Annotation Download screen.

NOTE By default, the source location is the Agilent Cloud system, or whichever local folder was

specified during installation (see the Data Download Option installation screen, step 19).

SureCall administrators can change the location from the Admin > Annotation Download

screen.

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Downloading Software Updates

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When an update is available, a dialog box automatically displays upon opening SureCall.

Figure 21 Updates Available message box

To automatically download these software updates:

1 Mark the Software update check box in the Updates Available dialog box. This will enable the Download button.

2 Click the Download button.

The Confirm message box opens asking you to confirm that you want to start downloading software update files.

3 Click OK to start the download process.

A Progress Status message displays. The application is unavailable for use during the software update download.

4 Once the download is complete, a Download Successfulmessage box opens, and counts down from 5 seconds to close the application. Skip the countdown by clicking OK.

5 A dialog box indicates that the application has been updated. Click OK to launch SureCall.

6 Upon logging in, a dialog box indicates that the Agilent SureCall application was upgraded successfully. Click OK to continue.

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2 Installation of SureCall 4.2.1 for Windows Software Upgrade Instructions

Upgrading a standalone version of SureCall 40

Upgrading SureCall on client computers 57

Uninstalling SureCall 65

This chapter provides instructions for users of SureCall 4.1.2 or 4.2.0 who want to upgrade to SureCall 4.2.1 while retaining all records currently in their SureCall database. It also contains instructions on uninstalling SureCall. The instructions in this chapter are specific for Windows computers.

If you want to upgrade from a previous version of SureCall to SureCall 4.2.1, but do not want to retain the records in your current database, first completely uninstall your existing version of SureCall (see Uninstall the client and server software for SureCall on page 65), then follow the instructions in Chapter 1, Installation of SureCall 4.2.1 for Windows Fresh Install Instructions on page 7.

Agilent Technologies

2 Installation of SureCall 4.2.1 for Windows Software Upgrade Instructions Upgrading a standalone version of SureCall

Upgrading a standalone version of SureCall

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These instructions are for users who are running an earlier standalone version of SureCall (i.e., the SureCall client software and server software are on a single computer) and want to upgrade to SureCall 4.2.1 while retaining the data in the existing database.

CAUTION The instructions provided here are strictly for upgrading from SureCall 4.1.2 or 4.2.0 to

SureCall 4.2.1.

If you are running SureCall 3.5, 4.0, 4.1.0, or 4.1.1, you cannot upgrade directly to SureCall

4.2.1. You must first upgrade to SureCall 4.1.2 or 4.2.0. Then, once SureCall 4.1.2 or 4.2.0 is

installed, follow the instructions here to upgrade to SureCall 4.2.1.

If you are running a version of SureCall prior to 3.5, you must first upgrade to SureCall 3.5,

then to SureCall 4.1.2 or 4.2.0. Then you can upgrade to SureCall 4.2.1.

Reboot your computer just prior to starting these instructions.

NOTE

1 Log on to the computer where you want to install a standalone version of SureCall 4.2.1. Use an account that has administrator permissions.

2 Double- click the Agilent SureCall 4.2.1.X.exe file to start the installation wizard. (See Download the software and release notes on page 10 for instructions on downloading the SureCall 4.2.1 installation files.)

The following message is displayed.

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Figure 22 InstallAnywhere dialog box preparing to install

The installation wizard starts.

Figure 23 Introduction screen for the installation wizard Windows

3 Read the introductory information. Pay particular attention to the information on RAM and hard disk space requirements.

4 Click Next.

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The following warning message opens, notifying you that if you continue with the software upgrade, any analysis jobs that are still running/waiting will be aborted.

Figure 24 Warning message Abort all running/waiting jobs

5 If the existing version of SureCall is still processing jobs, click No to avoid aborting those jobs. Otherwise, click Yes to continue with the upgrade.

Upon clicking Yes, the following message opens, notifying you that a version of SureCall client already exists on the local machine.

Figure 25 Information box Agilent SureCall already exists

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6 Click OK to proceed with uninstalling the existing Agilent SureCall client.

The following message box opens, notifying you that Agilent recommends restarting your computer prior to uninstalling the SureCall client. (If you did not reboot your computer just prior to starting step 1, do so now, then start again at step 1.)

Figure 26 Alert message box

7 Click Continue to continue uninstalling SureCall.

The uninstaller program opens to the Introduction screen.

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Figure 27 Uninstall Agilent SureCall Introduction screen Windows

8 Click Uninstall to proceed.

The Uninstall Options windows opens.

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Figure 28 Uninstall Agilent SureCall Uninstall Options screen Windows

9 Select Uninstall Specific Features, and click Next.

The Choose Product Features screen opens.

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Figure 29 Uninstall Agilent SureCall Choose Product Features screen Windows

10 In the top panel, mark the Client check box. Make sure that the Server check box is not marked.

11 Click Uninstall.

A message box opens asking you to confirm that you want to uninstall the SureCall client.

12 Click Yes in the message box to continue uninstalling.

The SureCall client is uninstalled. When the uninstallation is complete, the Uninstall Complete screen opens.

13 Click Done.

The uninstaller program closes and the SureCall 4.2.1 installation wizard opens to the License Agreement screen. You can now continue installing SureCall 4.2.1.

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Figure 30 License Agreement screen Windows

14 Read the license agreement. Select I accept the terms of the License Agreement and then click Next. (Click Previous to review information in a previous section.)

The Choose Install Set screen opens.

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Figure 31 Choose Install Set screen Windows

15 Click the icon next to Standalone to install both the SureCall 4.2.1 database server and client software on this computer.

16 Click Next.

The installation wizard looks for an existing version of SureCall server on your computer.

If the installation wizard successfully finds the existing version of SureCall server, a message box opens stating Agilent SureCall server already exists on the local machine. Click OK in the message box to continue upgrading the existing SureCall server to the SureCall 4.2.1 server. The Configure Proxy Settings screen opens and you can proceed to step 17.

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If the installation wizard cannot find an existing version of SureCall server on your computer, a message box opens stating Could not find Agilent SureCall server. You can either click Fresh Install to install a fresh SureCall 4.2.1 server (no data in the existing database will be retained), or click Upgrade to provide a valid Agilent SureCall server installation path. When you continue with the wizard, the Configure Proxy Settings screen opens and you can proceed to step 17.

Figure 32 Configure Proxy Settings screen Windows

17 If your institution requires you to connect to the internet through a proxy server, enter the information for the proxy server in the fields on the Configure Proxy Settings screen. Contact your network administrator to obtain the necessary information.

18 Click Next.

The Data Download Option screen opens.

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Figure 33 Data Download Option screen Windows

19 Select the default human genome build (hg19 or hg38) to be used as the reference in your analyses.

After installation is complete, the program begins downloading and installing the reference and annotation data for the selected genome build from Agilent Cloud storage.

Once SureCall installation is complete, SureCall administrators can download reference and annotation data for the non- default genome build from the Admin > Annotation Download screen of the software. This screen also has tools for changing the default genome build selection.

20 By default, immediately after you complete SureCall installation, SureCall will download from Agilent Cloud storage any reference and annotation data that is not already installed on the machine. If you prefer for SureCall to download and install the required data from a local storage folder or a storage folder saved to an external USB drive, enter the file path of that folder in the Provide Data Location field. You

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can type the file path directly into the field or click Choose to browse to the storage folder.

Leave the Provide Data Location field blank if you want SureCall to download the required data from Agilent Cloud storage.

If you received an external USB drive from Agilent containing the reference and annotation

NOTE data, plug in the USB drive to your computer and enter the file path of the drive into the

Provide Data Location field.

21 Click Next.

The Choose Install Folder screen opens.

Figure 34 Choose Install Folder screen Windows

22 By default, the program is installed in: C:\agilent\Agilent_SureCall_4.2.1.X (where X is the revision number). If you prefer to install the program in a different location, enter the file path of the desired folder into the provided field. You can type the file

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path directly into the field or click Choose to browse to the desired folder.

If you want to install SureCall in the default location, leave the default file path in the field.

NOTE The installation program folder must not be in the C:\Program Files folder due to

permissions settings within Windows 7.

23 Click Next.

The Choose Shortcut Folder screen opens.

Figure 35 Choose Shortcut Folder screen Windows

24 By default, program icons are installed in the Agilent SureCall program group on your computer. To select another location for the program icons, select the desired location (on the desktop, for example).

Agilent SureCall Installation Guide

Installation of SureCall 4.2.1 for Windows Software Upgrade Instructions 2 Upgrading a standalone version of SureCall

NOTE If more than one user plans to use SureCall 4.2.1 on this computer, select Create Icons for All Users. Otherwise, other users do not see the program icons.

Agilent SureCall Ins

25 Click Next.

The Pre- Installation Summary screen opens.

Figure 36 Pre-Installation Summary screen Windows

26 Review the installation setup information. If you want to change any of the settings, click Previous and go back and change the settings. To start the installation, click Install.

The Installing Agilent SureCall screen opens and remains open until the installation is complete.

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Figure 37 Installing Agilent SureCall screen Windows

When the SureCall installation is complete, the Install Complete screen opens.

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Figure 38 Install Complete screen Windows

27 Click Done.

The Download window opens and the program begins downloading and installing the reference and annotation data from Agilent Cloud storage (or from the folder you designated in the Data Download Option screen). Downloading the files requires an internet connection.

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Figure 39 Download screen

During this process, the Download screen remains open and displays which files have been downloaded and installed. Your system needs to be connected to the internet until the process is complete.

28 When the downloads are complete, click Close to close the Download dialog box.

If the download fails or does not complete, you can manually download the missing files from within SureCall. See Checking the data download on page 37.

Start the SureCall program, log in, and enter your license information. See Opening the SureCall 4.2.1 client software on page 32.

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Installation of SureCall 4.2.1 for Windows Software Upgrade Instructions 2 Upgrading SureCall on client computers

Upgrading SureCall on client computers

Agilent SureCall Ins

These instructions are for users who are running the SureCall client software only. Follow these steps to upgrade the client software to a new version.

Before upgrading to SureCall 4.2.1 on computers that are only running the client software,

NOTE upgrade to SureCall 4.2.1 on the computer that will run the database software. See

Upgrading a standalone version of SureCall on page 40.

NOTE Reboot your computer just prior to starting these instructions.

1 Double- click the Agilent SureCall 4.2.1.X.exe file to start the installation wizard.

The following message is displayed.

Figure 40 InstallAnywhere dialog box - preparing to install

The installation wizard starts.

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Figure 41 Introduction screen for the installation wizard Windows

2 Read the introductory information. Pay particular attention to the information on RAM and hard disk space requirements.

3 Click Next.

The following message is displayed, notifying you that a version of SureCall client already exists on the local machine.

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Figure 42 Information box Agilent SureCall already exists

4 Click OK to proceed with uninstalling the existing Agilent SureCall client.

The following message box opens, notifying you that Agilent recommends restarting your computer prior to uninstalling the SureCall client. If you did not reboot your computer just prior to starting step 1, do so now, then start again at step 1.

Figure 43 Alert message box

5 Click Continue to continue uninstalling SureCall.

The uninstaller program opens to the Introduction screen.

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Figure 44 Uninstall Agilent SureCall Introduction screen Windows

6 Click Uninstall to proceed.

A message box opens asking you to confirm that you want to uninstall the SureCall client.

7 Click Yes in the message box to continue uninstalling.

The SureCall client is uninstalled. When the uninstallation is complete, the Uninstall Complete screen opens.

8 Click Done.

The uninstaller program closes and the SureCall 4.2.1 installation wizard opens to the License Agreement screen. You can now continue installing SureCall 4.2.1.

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Figure 45 License Agreement screen Windows

9 Read the license agreement. Select I accept the terms of the License Agreement and then click Next. (Click Previous to review information in a previous section.)

The Choose Install Set screen opens.

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Figure 46 Choose Install Set screen Select Client Windows

10 On the Choose Install Set screen, select Client.

11 Click Next.

The Get Server Details screen opens.

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Figure 47 Get Server Details screen Windows

12 In the Server Name field, type the assigned computer name or IP address of the computer where you installed the SureCall 4.2.1 database server. (To find the computer name of your current computer, click Start > Control Panel > System.)

13 Accept the default Port, unless your system administrator tells you otherwise.

14 Click Next.

The installer immediately tests the connection to the specified database.

If incorrect database parameters are provided, or the PostgreSQL database service is not

NOTE running, a message is displayed. You can choose to continue the installation and change

database connection parameters when launching the client software. However, Agilent

recommends that you provide the correct database information during installation.

15 Continue the installation wizard. Follow the instructions for the installation wizard to configure the proxy settings, choose an install

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folder, choose a shortcut location, and start the installation. For information, see step 17 through step 27 in the section Upgrading a standalone version of SureCall on page 40.

Agilent SureCall Installation Guide

Installation of SureCall 4.2.1 for Windows Software Upgrade Instructions 2 Uninstalling SureCall

Uninstalling SureCall

Agilent SureCall Ins

This section provides instructions on uninstalling the SureCall software. On a computer in which a standalone copy of SureCall is installed, you can select to uninstall only the client software or both the client software and server software.

Uninstall the client and server software for SureCall

The Uninstall program for SureCall provides an easy way to remove the SureCall client, server, and PostgreSQL programs from your computer.

When you completely uninstall SureCall, the database, the data contained in the database,

CAUTION and the reference data, including the reference genome file, are all completely removed. Do

not uninstall the entire program unless you have backed up your database or no longer

wish to use it.

NOTE Reboot your computer just prior to starting these instructions.

1 Start the Uninstall Agilent SureCall.exe file, located in the Uninstall Agilent SureCall folder of your program folder.

Depending on which version of SureCall you are uninstalling, the following message box may open, notifying you that Agilent recommends restarting your computer prior to uninstalling SureCall. If you see this message box, click Continue.

Figure 48 Alert dialog box

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The uninstaller program starts.

2 Read the introductory information, and then click Next.

3 Read the warning information. You are cautioned not to stop the uninstaller once it has started to remove the programs. Click Next.

The Uninstall Options screen opens.

Figure 49 Uninstall Options screen Windows

4 Select Complete Uninstall and click Next.

If you are uninstalling version 3.5 or earlier, the Confirmation dialog box opens.

If you are uninstalling version 4.0 or later, a message box opens prompting you for the password for the Administrator account. Type the password into the provided field and click Authenticate. The Confirmation dialog box then opens.

Agilent SureCall Installation Guide

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Figure 50 SureCall Administrator Login dialog box Windows

5 In the Confirmation dialog box, click Yes to continue.

If you are uninstalling version 3.5 or earlier, the uninstallation process begins.

If you are uninstalling version 4.0 or later, a message box opens prompting you to confirm that you want to uninstall the server software, which will delete all existing data in the database. Click Delete all existing data to continue. The uninstallation process then begins.

6 When the uninstallation is complete, a message opens. Click Done.

The SureCall client program, server program and database, and PostgreSQL program were removed from your computer. Program folders and data folders (such as data output folders) created after installation are not removed.

Uninstall the SureCall client software only

Reboot your computer just prior to starting these instructions.

NOTE

1 Start the Uninstall Agilent SureCall.exe file, located in the Uninstall Agilent SureCall folder of your program folder.

Depending on which version of SureCall you are uninstalling, the following message box may open, notifying you that Agilent recommends restarting your computer prior to uninstalling SureCall. If you see this message box, click Continue.

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Figure 51 Alert dialog box

The uninstaller program starts.

2 Read the introductory information, and then click Next.

3 Read the warning information. You are cautioned not to stop the uninstaller once it has started to remove the programs. Click Next.

The Uninstall Options screen opens.

Figure 52 Uninstall Options screen select Uninstall Specific Features Windows

4 Select Uninstall Specific Features and click Next.

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The Choose Product Features screen opens.

Figure 53 Choose Product Features screen mark Client Windows

5 In the Choose Product Features screen, mark Client. When the Client check box is selected, only the client program is removed from the computer. The client program folder and any data folders created after installation are not removed.

The Uninstall button becomes active.

Do not select Server unless you want to remove client and server software completely,

CAUTION including the database, from your computer.

6 Click Uninstall.

In the Confirmation dialog box that opens, click Yes to continue.

7 When the uninstallation has completed, click Done.

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Agilent SureCall Installation Guide

3 Installation of SureCall 4.2.1 for Macintosh Fresh Install Instructions

Installing Java Standard Edition 11 (Java SE 11) 72

Preparing for installation 74

Installing a standalone version of SureCall 4.2.1 Macintosh 76

Opening the SureCall 4.2.1 client software 92

Adding a SureDesign user name and password 94

Checking the data download 95

This chapter shows you how to install and get started using SureCall 4.2.1 on computers running the macOS Catalina operating system.

NOTE Versions of SureCall prior to version 4.2.1 are not compatible with the macOS Catalina

operating system. Please email informatics_support@agilent.com for advice on upgrading

from a previous version of SureCall to SureCall 4.2.1 on a Macintosh computer.

For instructions on installing SureCall 4.2.1 on a Windows computer, see Chapter 1, Installation of SureCall 4.2.1 for Windows Fresh Install Instructions on page 7.

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3 Installation of SureCall 4.2.1 for Macintosh Fresh Install Instructions Installing Java Standard Edition 11 (Java SE 11)

Installing Java Standard Edition 11 (Java SE 11)

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The installer for the Macintosh version of SureCall 4.2.1 can only run on Macintosh computers that have Java SE 11 installed. Check your computer to see which versions of Java SE, if any, are installed (see To check which versions of Java are installed on page 72). If your computer does not have Java SE 11, follow the instructions in To install Java SE 11 on page 73.

The Macintosh version of SureCall 4.2.1 also requires AdoptOpenJDK version 11.0.4. If it is

To check which versions of Java are installed

NOTE not already installed on your Macintosh computer, it will automatically be installed during

installation of SureCall 4.2.1.

1 Open the System Information.

a In the Applications folder, open the Utilities folder.

b Double- click the System Information icon.

2 Under Software, click Installations.

The screen displays the completed installations. If Java SE 11 is installed, it is listed as shown in Figure 54.

Figure 54 Java SE 11 installation as displayed in System Information

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Installation of SureCall 4.2.1 for Macintosh Fresh Install Instructions 3 Installing Java Standard Edition 11 (Java SE 11)

To install Java SE 11

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If your Macintosh computer does not already have Java SE 11installed, you need to install it before you can install SureCall.

1 Launch an internet browser and go to the webpage: www.oracle.com/in/java/technologies/javase- jdk11- downloads.html.

2 Download the Java SE 11 installer to the desired location on your computer.

3 When download is complete, launch the Java SE 11 installer and follow the prompts to install the software.

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Preparing for installation

Download the software and release notes

74

1 Go to www.agilent.com/en/download- software- surecall.

2 Click Download Software.

3 Click the Download link for the Macintosh version of the software.

4 Select Save File to save the installer zip folder to your computer. (This folder contains large files. Depending on your internet connection speed, the download can take a long time.)

5 Browse to a location where you want to save the installer zip folder, and then click Save. (Do not start the installation at this time.)

6 Return to www.agilent.com/en/download- software- surecall and click Download Software again.

7 Click the Download link for the Release Notes.

8 Click Save As.

9 Browse to a location where you want to save the release notes.

10 Click Save.

You will also need to download the installer for the sequence alignment tools from the

NOTE www.agilent.com/en/download-software-surecall website. See Installing Sequence

Alignment Tools (GenAligners) on page 98 for instructions.

Agilent SureCall Installation Guide

Installation of SureCall 4.2.1 for Macintosh Fresh Install Instructions 3 Preparing for installation

Check system requirements before you start

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Check to make sure that your computer systems meet the following requirements. See Table 3 for minimum and recommended requirements.

Set up permissions for installer and users

Table 3 System requirements for running SureCall 4.2.1 on Macintosh computers

Operating system macOS Catalina

Programs Any program that enables you to open PDF files (for example, Adobe Reader)

Java SE 11 (see Installing Java Standard Edition 11 (Java SE 11) on page 72)

Processor Minimum: > 2.0 GHz dual-core Intel Core i5

Recommended: > 2.5 GHz dual-core Intel Core i7

Working memory (RAM) Without aligners installed: 8 GB

With aligners installed: 12 GB (16 GB recommended)

Hard disk space 500 GB (50 GB for genome reference data and annotation data and 450 GB for your

sequencing data)

Display Resolution 1280 x 768 or higher

Make sure that the user account used to install the SureCall 4.2.1 software has administrator permissions on the installation computer.

Make sure that every user account running the SureCall 4.2.1 software has read/write permissions to the following:

The computer where the client software is installed

The installation folder on the computer where the database server is installed

The folders where input data for analyses (e.g., BAM files) will be stored

The folder where output data (e.g., reports) will be stored

The way you set permissions varies between operating systems. Contact your network administrator for help in checking or changing user account permissions. If the correct user account permissions are not set correctly, the software will fail to install or run properly.

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SureCall consists of two parts: a PostgreSQL database server and the client software. To run SureCall on a Macintosh computer, you must install SureCall as a standalone program, which requires installing both the database server and client software on the same computer. The client is the program that your run when you want to use SureCall. The database server runs silently in the background. While the Windows version of SureCall allows you to install additional copies of the client software on client computers that have network access to the database computer, the Macintosh version does not support that setup.

This section includes detailed instructions and important notes for installing SureCall 4.2.1 as a standalone program.

1 Log on to the computer where you want to install SureCall 4.2.1. Use an account that has administrator permissions.

2 Locate the installation program you downloaded in Step 1, Download the software and release notes on page 74. Double- click the Agilent SureCall Edition 4.2.1.X.zip folder to extract the installer.

3 Double- click the Agilent SureCall Edition 4.2.1.X icon to start the installation wizard.

The Introduction screen opens.

NOTE If you see a warning message stating that the file cannot be opened because Apple cannot

check it for malicious software, close warning message then go to System Preferences > Security & Privacy. In the Allow apps downloaded from section is a message about

blocking the Agilent SureCall installer. click Open Anyway.

At this point, repeat step 3. This time when the warning message opens, click Open to

proceed with the installation.

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Figure 55 Introduction screen for the installation wizard Macintosh

4 Read the introductory information. Pay particular attention to the information on RAM and hard disk space requirements.

5 Click Next.

The License Agreement screen opens.

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Figure 56 License Agreement screen Macintosh

6 Read the license agreement. Select I accept the terms of the License Agreement and then click Next. (Click Previous to review information in a previous section.)

The Choose Install Set screen opens.

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Figure 57 Choose Install Set screen Macintosh

7 Click the icon next to Standalone to install both the database server and client software on this computer.

8 Click Next.

The Enter Domain Properties screen opens.

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Figure 58 Enter Domain Properties screen Macintosh

9 If only the administrator will be accessing SureCall from this computer, or if the computer is a local machine, click Next. The Enter Administrator Details screen opens, and you can proceed to step 10.

If the computer is on a domain, and more than one user plans to use SureCall on this computer, configure the domain properties using the instructions in the following substeps.

a Mark Configure Domain Properties.

b Using the domain properties for your system, complete the fields for User Domain, User DNS Domain, LDAP Server, Global Catalog Server Port, and LDAP Port.

c Click Next.

The Enter Administrator Details screen opens.

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If you see a warning message titled Domain validation failed, click OK in the massage box,

NOTE and then click Previous in the installer to return to the Enter Domain Properties screen.

Repeat step b above with the correct domain properties. Do not proceed with the

installation until you enter the domain properties and do not receive the Domain validation failed warning message.

Figure 59 Enter Administrator Details screen Macintosh

10 In the User Account field, type the username of the person who will be the administrator for the SureCall software, using the format shown in the examples below.

For domain user: DOMAIN\username

For local machine: username

11 To set up additional SureCall users, mark the check box labeled Add SureCall Users. In the Password field that appears, type the password for the SureCall administrator account.

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If you do not want to set up new users at this time, proceed directly to step 16 on page 83. Note that the administrator can set up new users from within SureCall once installation is complete.

To set up SureCall users during installation, you need to have entered the domain properties

NOTE back in step 9.

12 Click Next.

The Add SureCall Users screen opens.

Figure 60 Add SureCall Users screen Macintosh

13 The Add SureCall Users screen lists all of the users in the domain. Mark the check box next to the users that you want to add to the SureCall database.

To search for a user, type the user name into the search box at the top of the screen.

14 Click Next.

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The Add SureCall Users screen advances to the step for configuring user roles.

Figure 61 Add SureCall Users screen Configure roles step Macintosh

15 For each user listed on the screen, select a role in the Roles drop- down list. The default selection is Technician.

Administrators can also edit user roles from within SureCall once installation is complete.

16 Click Next.

The Configure Proxy Settings screen opens.

Figure 62 Configure Proxy Settings screen Macintosh

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17 If your institution requires you to connect to the internet through a proxy server, enter the information for the proxy server in the fields on the Configure Proxy Settings screen. Contact your network administrator to obtain the necessary information.

18 Click Next.

The Data Download Option screen opens.

Figure 63 Data Download Option screen Macintosh

19 Select the default human genome build (hg19 or hg38) to be used as the reference in your analyses.

After installation is complete, the program begins downloading and installing the reference and annotation data for the selected genome build from Agilent Cloud storage.

Once SureCall installation is complete, SureCall administrators can download reference and annotation data for the non- default genome build from the Admin > Annotation Download screen of the software. This screen also has tools for changing the default genome build selection.

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20 By default, SureCall will download and install the required reference and annotation data from Agilent Cloud storage immediately after you complete SureCall installation. If you prefer for SureCall to download and install the required data from a local storage folder or a storage folder saved to an external USB drive, enter the file path of that folder in the Provide Data Location field. You can type the file path directly into the field or click Choose to browse to the storage folder.

Leave the Provide Data Location field blank if you want SureCall to download the required data from Agilent Cloud storage.

If you received an external USB drive from Agilent containing the reference and annotation

NOTE data, plug in the USB drive to your computer and enter the file path of the drive into the

Provide Data Location field.

21 Click Next.

The Choose Install Folder screen opens.

Figure 64 Choose Install Folder screen Macintosh

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22 By default, the program is installed in the Agilent SureCall Edition 4.2.1.X folder (where X is the revision number) in the Agilent folder on the Macintosh HD disk. Leave the default folder in place, or click Choose to select a new location where you want to install the SureCall program folder. Within this folder, one folder is created for the server software and one folder is created for the client software.

23 Click Next.

The Common Storage Option screen opens.

Figure 65 Common Storage option screen Macintosh

24 By default, the common storage files, including the output files for SureCall analyses, are stored in /Applications/Agilent/Agilent_SureCall_4.2.1.X/Server/CommonStorage (where X is the revision number). If you prefer to save the files to a different location, mark the check box labeled Change Common Storage Location. In the field that appears, enter the file path of the desired folder. You can type the file path directly into the field or click Choose to browse to the desired folder.

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If you want to save the common storage files to the default location, leave the check box unmarked.

25 Click Next.

The Choose Alias Folder screen opens.

Figure 66 Choose Alias Folder screen Macintosh

26 By default, program icon is installed on the Desktop of your computer. To select another location for the program icon, select the desired location (In the Dock, for example) and then click Next.

The Pre- Installation Summary screen opens.

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Figure 67 Pre-Installation Summary screen Macintosh

27 Review the installation setup information. If you want to change any of the settings, click Previous and go back and change the settings. To start the installation, click Install.

The Installing Agilent SureCall Edition 4.2.1.X screen opens.

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Figure 68 Installing Agilent SureCall screen Macintosh

28 During the SureCall installation process, the PSQL Service installs a new helper tool. When prompted with the message box shown below, enter your username and password and click Install Helper.

Figure 69 PSQL Service prompt

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After clicking Install Helper, you may see a message stating that the iCloud Drive may not

NOTE work properly. Click OK to close the message and continue the installation.

The Installing PSQLService window opens displaying the progress of the helper tool install. The windows closes when installation is complete.

Figure 70 Installing PSQLService window

When the SureCall installation is complete, the Install Complete screen opens.

29 Click Done.

The Download window opens and the program begins downloading and installing the reference and annotation data from Agilent Cloud storage (or from the folder you designated in the Data Download Option screen).

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Figure 71 Download screen

During this process, the Download screen remains open and displays which files have been downloaded and installed. Your system needs to be connected to the internet until the process is complete.

Depending on your internet connection, the download process can take anywhere from 15

NOTE minutes to 2 hours.

30 When the downloads are complete, click Close to close the Download dialog box.

If the download fails or does not complete, you can manually download the missing files from within SureCall. See Checking the data download on page 95.

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Opening the SureCall 4.2.1 client software

92

After you install the SureCall database server and client program, start the program.

1 Double- click the SureCall 4.2.1 icon to open the program.

NOTE How you start the program depends on the choice you made for the Alias or Install Folder

during installation of the client software.

When the program first opens, the top right panel of the screen displays the login area. The name and domain for the administrator set during installation appear in the fields.

Figure 72 Login area

2 Type your user name and password into the fields. Once logged in, administrators can add additional users and assign their roles.

If you need to change the domain, expand the drop- down list next to Domain and select the correct domain.

3 Click OK.

After you log in for the first time, the Enter License dialog box opens.

4 If you do not already have the license file saved to your computer, click Request for license to open the Agilent website to the SureCall license

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request page. Complete the fields in the request form to obtain a SureCall software license.

The license is contained in a text file.

5 At the bottom of the dialog box, click Browse.

The Open dialog box opens.

6 Browse to the saved license file. Select the file and click Open.

The program loads the content of the file into the text area on the Enter License dialog box.

7 Click OK.

The SureCall program opens.

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Before you can download a design file from SureDesign into SureCall, you must add the SureDesign account information.

1 Go to the SureDesign Settings screen in SureCall.

a At the top of the program window, click Admin.

b On the left side of the screen, click SureCall Connector.

c Click the SureDesign tab near the top of the screen.

2 Type the user name for the SureDesign account into the SureDesign Username field.

In SureDesign, the user name is the e- mail address of the user.

3 In the SureDesign Password field, type the password for the SureDesign account.

4 Click Apply.

5 Click Test Connection.

A message box opens notifying you if the connection test succeeded or failed.

If the connection test passes, you can download design files from SureDesign into SureCall using the tools on the Supporting Files screen.

If the connection test fails, go to the SureDesign website (www.agilent.com/genomics/suredesign) and try logging in. If the login fails, you can reset the password or register for a new account.

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When you first installed SureCall, the program automatically downloaded the necessary reference and annotation files from Agilent Cloud storage or from a specified local folder or drive (see step 29 through step 30 on page 90.) Downloading the files requires an internet connection and a minimum of 20 GB of disk space.

Before you start running analyses in SureCall, make sure that the program successfully completed the data download process.

1 Go to the Annotation Download screen in SureCall.

a At the top of the program window, click Admin.

b On the left side of the screen, click Annotation Download.

2 Click Refresh Annotation Status.

3 In the message box that opens, click Yes to continue.

The program obtains the status of the data file downloads and displays the statuses in a table on the Annotation Download screen.

4 Check the status of the downloads.

If all files were successfully downloaded. the top right corner of the screen displays the message All data files downloaded successfully.

If some files were not successfully downloaded, click Start Download. The program will connect to the Agilent Cloud storage system, or the local folder or drive specified during SureCall installation, to download the missing files.

The source location for the files is specified on the Admin > Annotation Download screen.

NOTE By default, the source location is the Agilent Cloud system, or whichever local folder was

specified during installation (see the Data Download Option installation screen, step 19).

SureCall administrators can change the location from the Admin > Annotation Download

screen.

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Agilent SureCall Installation Guide

4 Installation of Sequence Alignment Tools

Installing Sequence Alignment Tools (GenAligners) 98

Step 1. Uninstall the previous version of GenAligners (if

applicable) 98

Step 2. Download the GenAligners installer from the Agilent

website 98

Step 3. Install the alignment tools on your computer 99

This chapter shows you how to install the sequence alignment tools provided by Agilent for use with SureCall 4.2.1.

Agilent Technologies

4 Installation of Sequence Alignment Tools Installing Sequence Alignment Tools (GenAligners)

Installing Sequence Alignment Tools (GenAligners)

98

In order to use SureCall to analyze unaligned sequencing files, you must download and install the compatible alignment tools provided by Agilent. SureCall uses the Burrows- Wheeler aligner (BWA) for alignment of Illumina data (Illumina GA, HiSeq, and MiSeq).

This section provides instructions for downloading and installing the alignment tools.

Step 1. Uninstall the previous version of GenAligners (if applicable)

If you have an older version of the GenAligners application installed on your system, uninstall the older version before installing the new version.

Windows computers

On Windows computers, SureCall 4.2.1 is not compatible with any version of GenAligners prior to version 3.0. To check the version number of your GenAligners application, open the installation folder (default installation folder is C:\Program Files\GenAligners), then open the file version.txt. If you are not running version 3.0, uninstall GenAligners from the Windows Control Panel. If you cannot find the utility for uninstalling, search for uninstall a program within the Control Panel search field.

Macintosh computers

On Macintosh computers, SureCall 4.2.1 is only compatible with the newest version of the GenAligners application (released in May 2019). Uninstall the existing version of GenAligners by deleting the application.

Step 2. Download the GenAligners installer from the Agilent website

1 Go to www.agilent.com/en/download- software- surecall.

2 Under Download Needed Sequence Aligners, click the appropriate download link (Windows or Macintosh).

3 The installer package for the GenAligners software is saved to your computer in the default location for downloaded files.

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Step 3. Install the alignment tools on your computer

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1 Launch the GenAligners installer package.

The GenAligners Setup wizard opens to the Welcome screen.

Figure 73 GenAligners Setup - Welcome screen

2 Click Next.

The End- User License Agreement window opens.

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Figure 74 GenAligners Setup - End-User License Agreement screen

3 Mark the check box next to I accept the term in the License Agreement. Click Next.

The Destination Folder window opens.

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Figure 75 GenAligners Setup - Destination Folder screen

4 By default, the alignment tools are installed in C:\ProgramFiles\GenAligners. If you prefer to install the program in a different location, enter the file path of the desired folder into the provided field. You can type the file path directly into the field or click Change to browse to the desired folder.

If you want to install SureCall in the default location, leave the default file path in the field.

5 Click Next.

The Ready to Install window opens.

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Figure 76 GenAligners Setup - Ready to Install screen

6 Click Install.

The Installing GenAligners screen opens and remains open until the installation is complete.

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Figure 77 GenAligners Setup - Installing GenAligners screen

When the installation is complete, the Completed the GenAligners Setup Wizard screen opens.

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Figure 78 GenAligners Setup - Completed the GenAligners Setup Wizard screen

7 Click Finish to close the wizard.

Agilent recommends restarting your computer after installation of the sequence alignment

NOTE tools is complete. SureCall will automatically connect to the alignment tools when you

restart the program.

Agilent SureCall Installation Guide

www.agilent.com

In this book

This book gives you instructions for installing SureCall 4.2.1.

Manualsnet FAQs

If you want to find out how the SureCall 4.2.1 Agilent works, you can view and download the Agilent SureCall 4.2.1 Sequencer Installation Guide on the Manualsnet website.

Yes, we have the Installation Guide for Agilent SureCall 4.2.1 as well as other Agilent manuals. All you need to do is to use our search bar and find the user manual that you are looking for.

The Installation Guide should include all the details that are needed to use a Agilent SureCall 4.2.1. Full manuals and user guide PDFs can be downloaded from Manualsnet.com.

The best way to navigate the Agilent SureCall 4.2.1 Sequencer Installation Guide is by checking the Table of Contents at the top of the page where available. This allows you to navigate a manual by jumping to the section you are looking for.

This Agilent SureCall 4.2.1 Sequencer Installation Guide consists of sections like Table of Contents, to name a few. For easier navigation, use the Table of Contents in the upper left corner.

You can download Agilent SureCall 4.2.1 Sequencer Installation Guide free of charge simply by clicking the “download” button in the upper right corner of any manuals page. This feature allows you to download any manual in a couple of seconds and is generally in PDF format. You can also save a manual for later by adding it to your saved documents in the user profile.

To be able to print Agilent SureCall 4.2.1 Sequencer Installation Guide, simply download the document to your computer. Once downloaded, open the PDF file and print the Agilent SureCall 4.2.1 Sequencer Installation Guide as you would any other document. This can usually be achieved by clicking on “File” and then “Print” from the menu bar.