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Agilent SureCall 3.0
Installation Guide
For Research Use Only. Not for Use in Diagnostic
Procedures.
Agilent Technologies
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© Agilent Technologies, Inc. 2015
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G4890-90003
Edition
Revision B0, June 2015
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Agilent SureCall Installation Guide
In This Guide…
This Installation Guide provides instructions for installing
SureCall 3.0.
1
Installation of SureCall 3.0 for Windows – Fresh Install
Instructions
This chapter provides instructions for new SureCall users on
how to install and get started using SureCall 3.0 on
computers running the Windows 7 Enterprise or Windows 7
Professional operating system.
2
Installation of SureCall 3.0 for Windows – Software Upgrade
Instructions
This chapter provides instructions for users of SureCall 2.0
or 2.1 who want to upgrade to SureCall 3.0 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 3.0 for Macintosh – Fresh Install
Instructions
This chapter shows you how to install and get started using
SureCall 3.0 on computers running the Macintosh OS X
Mountain Lion or Mavericks operating system.
4
Installation of SureCall 3.0 for Macintosh – Software Upgrade
Instructions
This chapter provides instructions for Macintosh users of
SureCall 2.0 or 2.1 who want to upgrade to SureCall 3.0
while retaining all records currently in their SureCall
database. It also contains instructions on uninstalling
SureCall. The instructions in this chapter are specific for
Macintosh computers running the Macintosh OS X Mountain
Lion operating system.
Agilent SureCall Installation Guide
3
5
Installation of Sequence Alignment Tools
This chapter shows you how to install the sequence
alignment tools provided by Agilent for use with SureCall
3.0.
4
Agilent SureCall Installation Guide
1
Installation of SureCall 3.0 for Windows – Fresh Install Instructions
7
Preparing for installation 8
Download the software and release notes 8
Check system requirements before you start 9
Set up permissions for installer and users 10
Adjust user account settings 10
Installing a standalone version of SureCall 3.0 – Windows
11
Installing SureCall 3.0 client on additional computers – Windows
Opening the SureCall 3.0 client software
Adding users and assign roles
29
31
Adding a SureDesign user name and password
Checking the data download
Downloading Software Updates
2
33
34
35
Installation of SureCall 3.0 for Windows – Software Upgrade Instructions
Upgrading a standalone version of SureCall
Upgrading SureCall on client computers
37
38
54
Uninstalling SureCall 62
Uninstall the client and server software for SureCall
Uninstall the SureCall client software only 64
3
26
62
Installation of SureCall 3.0 for Macintosh – Fresh Install Instructions
Installing Java Standard Edition (Java SE) 68
To check which versions of Java are installed
To install Java SE 6 68
To install Java SE 8 69
67
68
Preparing for installation 71
Download the software and release notes 71
Check system requirements before you start 72
Agilent SureCall Installation Guide
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Set up permissions for installer and users
73
Installing a standalone version of SureCall 3.0 – Macintosh
Opening the SureCall 3.0 client software
90
Adding a SureDesign user name and password
Checking the data download
4
5
74
92
93
Installation of SureCall 3.0 for Macintosh – Software Upgrade Instructions
Upgrading a standalone version of SureCall – Macintosh
96
Uninstalling SureCall – Macintosh 107
Uninstall the client and server software for SureCall
Uninstall the SureCall client software only 108
107
Installation of Sequence Alignment Tools
111
Installing Sequence Alignment Tools 112
Step 1. Download the GenAligners installer from the Agilent website
Step 2. Install the alignment tools on your computer 112
6
95
112
Agilent SureCall Installation Guide
1
Installation of SureCall 3.0 for Windows
– Fresh Install Instructions
Preparing for installation 8
Installing a standalone version of SureCall 3.0 – Windows 11
Installing SureCall 3.0 client on additional computers – Windows 26
Opening the SureCall 3.0 client software 29
Adding users and assign roles 31
Adding a SureDesign user name and password 33
Checking the data download 34
Downloading Software Updates 35
This chapter provides instructions for new SureCall users on how to
install and get started using SureCall 3.0 on computers running the
Windows 7 Enterprise or Windows 7 Professional operating system.
For instructions on upgrading from a previous version of SureCall to
SureCall 3.0, see Chapter 2, “Installation of SureCall 3.0 for Windows –
Software Upgrade Instructions” on page 37.
For instructions on installing SureCall 3.0 on a Macintosh computer, see
Chapter 3, “Installation of SureCall 3.0 for Macintosh – Fresh Install
Instructions” on page 67.
Agilent Technologies
1
Installation of SureCall 3.0 for Windows – Fresh Install Instructions
Preparing for installation
Preparing for installation
Download the software and release notes
1 Go to http://www.agilent.com/genomics/surecall_soft.
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 http://www.agilent.com/genomics/surecall_soft.
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.
NOTE
8
You will also need to download the installer for the sequence alignment tools from the
http://www.agilent.com/genomics/surecall_soft website.. See “Installing Sequence
Alignment Tools” on page 112 for instructions.
Agilent SureCall Installation Guide
Installation of SureCall 3.0 for Windows – Fresh Install Instructions
Preparing for installation
1
Check system requirements before you start
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 1 for minimum requirements. See
Table 2 for recommended requirements.
Table 1
Minimum requirements for running SureCall on Windows computers
Operating system
64-bit Windows 7 Enterprise or Windows 7 Professional
Programs
Any program that enables you to open PDF files (for example, Adobe Reader)
Processor
> 2 GHz
Working memory (RAM)
Without aligners installed: 8 GB
With aligners installed: 12 GB
Hard disk space
470 GB (20 GB for genome reference data and annotation data and 450 GB for your
sequencing data)
Display Resolution
1280 x 768 or higher
Table 2
Recommended requirements for running SureCall on Windows computers
Operating system
64-bit Windows 7 Enterprise or Windows 7 Professional
Programs
Any program that enables you to open PDF files (for example, Adobe Reader)
Processor
> 3 GHz, 8-core
Working memory (RAM)
Without aligners installed: 8 GB
With aligners installed: 16 GB
Hard disk space
470 GB (20 GB for genome reference data and annotation data and 450 GB for your
sequencing data)
Display Resolution
1280 x 768 or higher
Agilent SureCall Installation Guide
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1
Installation of SureCall 3.0 for Windows – Fresh Install Instructions
Preparing for installation
Set up permissions for installer and users
• Make sure that the user account used to install the SureCall 3.0
software has administrator permissions on the installation computer.
• Make sure that every user account running the SureCall 3.0 software
has read/write permissions in the computer where the client software
is installed. In addition, users must have read/write permissions in the
installation folder of the computer where the database server is
installed.
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.
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Installation of SureCall 3.0 for Windows – Fresh Install Instructions
Installing a standalone version of SureCall 3.0 – Windows
1
Installing a standalone version of SureCall 3.0 – Windows
SureCall consists of two parts: a PostgreSQL database server and the
client software. This section includes detailed instructions and important
notes for installing SureCall 3.0 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 3.0 client on additional computers – Windows” on page 26.
NOTE
Only one copy of the server software is installed. To run the client software, the database
server must be installed. The client is the program you run when you want to use SureCall.
You can run the client program on the same computer as the server, or from any other
computer with the client program installed. After installation, the database server software
runs silently in the background and manages the shared database for all SureCall 3.0 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 3.0. Use an account that has administrator permissions.
2 Locate the installation program you downloaded in “Download the
software and release notes” on page 8. Double-click the Agilent
SureCall 3.0.XX.exe file to start the installation wizard.
The following message is displayed.
Figure 1
InstallAnywhere dialog box - preparing to install
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Installing a standalone version of SureCall 3.0 – Windows
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 License Agreement screen opens.
12
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Figure 3
1
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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Installation of SureCall 3.0 for Windows – Fresh Install Instructions
Installing a standalone version of SureCall 3.0 – Windows
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 following message box opens notifying you that the installation
wizard could not detect an existing copy of the SureCall server on the
local computer.
14
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Figure 5
1
Confirm message box – Could not find Agilent SureCall server
8 Click Fresh Install in the message box.
The Enter Administrator Details screen opens.
Figure 6
Enter Administrator Details screen – Windows
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Installation of SureCall 3.0 for Windows – Fresh Install Instructions
Installing a standalone version of SureCall 3.0 – Windows
9 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 3.0 software, type the correct user, using
the one of the formats shown below.
For domain user: DOMAIN\username
For local machine: MACHINENAME\username
10 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 16 on page 17. Note that administrators can set up new users from
within SureCall once installation is complete (see “Adding users and
assign roles” on page 31).
11 Click Next.
The Add SureCall Users screen opens.
Figure 7
16
Add SureCall Users screen – Windows
Agilent SureCall Installation Guide
Installation of SureCall 3.0 for Windows – Fresh Install Instructions
Installing a standalone version of SureCall 3.0 – Windows
1
12 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.
13 Click Next.
14 The Add SureCall Users screen advances to the step for configuring
user roles.
Figure 8
Add SureCall Users screen – Configure roles step – Windows
15 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.
16 Click Next.
The Configure Proxy Settings screen opens.
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Figure 9
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.
18
Agilent SureCall Installation Guide
Installation of SureCall 3.0 for Windows – Fresh Install Instructions
Installing a standalone version of SureCall 3.0 – Windows
Figure 10
1
Data Download Option screen – Windows
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.
Leave the Provide Data Location field blank if you want SureCall to
download the required data from Agilent Cloud storage.
NOTE
If you received an external USB drive from Agilent containing the reference and annotation
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.
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Installation of SureCall 3.0 for Windows – Fresh Install Instructions
Installing a standalone version of SureCall 3.0 – Windows
Figure 11
Choose Install Folder screen – Windows
21 By default, the program is installed in:
C:\agilent\Agilent_SureCall_3.0.XX (where XX 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.
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.
22 Click Next.
The Choose Shortcut Folder screen opens.
20
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Installation of SureCall 3.0 for Windows – Fresh Install Instructions
Installing a standalone version of SureCall 3.0 – Windows
Figure 12
1
Choose Shortcut Folder screen – Windows
23 By default, program icons are installed in the Agilent SureCall program
group on your computer (where XX is the revision number). 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 3.0 on this computer, select Create Icons for All
Users. Otherwise, other users do not see the program icons.
24 Click Next.
The Pre-Installation Summary screen opens.
Agilent SureCall Installation Guide
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Installation of SureCall 3.0 for Windows – Fresh Install Instructions
Installing a standalone version of SureCall 3.0 – Windows
Figure 13
Pre-Installation Summary screen – Windows
25 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.
22
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Installation of SureCall 3.0 for Windows – Fresh Install Instructions
Installing a standalone version of SureCall 3.0 – Windows
Figure 14
1
Installing Agilent SureCall screen – Windows
When the SureCall installation is complete, the Install Complete screen
opens.
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Installation of SureCall 3.0 for Windows – Fresh Install Instructions
Installing a standalone version of SureCall 3.0 – Windows
Figure 15
Install Complete screen – Windows
26 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).
24
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Installation of SureCall 3.0 for Windows – Fresh Install Instructions
Installing a standalone version of SureCall 3.0 – Windows
Figure 16
1
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.
NOTE
Depending on your internet connection, the download process can take anywhere from 15
minutes to 2 hours.
27 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 34.
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Installation of SureCall 3.0 for Windows – Fresh Install Instructions
Installing SureCall 3.0 client on additional computers – Windows
Installing SureCall 3.0 client on additional computers – Windows
To use other computers to run SureCall 3.0 client software (with a shared
database), install the client software on each of the computers.
NOTE
Before installing SureCall 3.0 client, install a standalone version of SureCall 3.0 on the
computer that will run the database software. See “Installing a standalone version of
SureCall 3.0 – Windows” on page 11.
1 On each computer that you want to run the SureCall 3.0 program, run
the installation wizard, as described in “Installing a standalone version
of SureCall 3.0 – Windows” on page 11.
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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Agilent SureCall Installation Guide
Installation of SureCall 3.0 for Windows – Fresh Install Instructions
Installing SureCall 3.0 client on additional computers – Windows
Figure 18
1
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 3.0 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.
NOTE
If incorrect database parameters are provided, or the PostgreSQL database service is not
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
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Installation of SureCall 3.0 for Windows – Fresh Install Instructions
Installing SureCall 3.0 client on additional computers – Windows
shortcut location, and start the installation. For information, see step 9
through step 27 in the section “Installing a standalone version of
SureCall 3.0 – Windows” on page 11.
28
Agilent SureCall Installation Guide
Installation of SureCall 3.0 for Windows – Fresh Install Instructions
Opening the SureCall 3.0 client software
1
Opening the SureCall 3.0 client software
After you install the SureCall database server and client programs as
described in this manual, start the program.
1 Double-click the SureCall 3.0 icon, or select SureCall 3.0 from the
Windows Start menu.
NOTE
How you start the program depends on the choice you made for Shortcut Folder during
installation.
After you start the program, the Login screen opens. The name and
domain for the administrator set during installation appear in the
dialog box.
Figure 19
Login screen
2 Type your user name and password into the fields. After the software
is started, 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.
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Installation of SureCall 3.0 for Windows – Fresh Install Instructions
Opening the SureCall 3.0 client software
3 Click OK.
After you log in for the first time, the following dialog box opens.
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 opens.
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Installation of SureCall 3.0 for Windows – Fresh Install Instructions
Adding users and assign roles
1
Adding users and assign roles
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.
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Installation of SureCall 3.0 for Windows – Fresh Install Instructions
Adding users and assign roles
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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Installation of SureCall 3.0 for Windows – Fresh Install Instructions
Adding a SureDesign user name and password
1
Adding a SureDesign user name and password
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 SureDesign Settings.
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 3.0 for Windows – Fresh Install Instructions
Checking the data download
Checking the data download
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.
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.
NOTE
34
The source location for the files is specified on the Admin > Annotation Download screen.
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.
Agilent SureCall Installation Guide
Installation of SureCall 3.0 for Windows – Fresh Install Instructions
Downloading Software Updates
1
Downloading Software Updates
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 Successful message 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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Downloading Software Updates
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Installation of SureCall 3.0 for Windows
– Software Upgrade Instructions
Upgrading a standalone version of SureCall 38
Upgrading SureCall on client computers 54
Uninstalling SureCall 62
This chapter provides instructions for users of SureCall 2.0 or 2.1 who
want to upgrade to SureCall 3.0 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
3.0, 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 62), then follow the
instructions in Chapter 1, “Installation of SureCall 3.0 for Windows –
Fresh Install Instructions” on page 37.
If you want to upgrade to SureCall 3.0 from a previous version on a
Macintosh computer, then see Chapter 4, “Installation of SureCall 3.0 for
Macintosh – Software Upgrade Instructions” on page 37.
Agilent Technologies
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Installation of SureCall 3.0 for Windows – Software Upgrade Instructions
Upgrading a standalone version of SureCall
Upgrading a standalone version of SureCall
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 3.0 while
retaining the data in the existing database.
NOTE
You can upgrade from SureCall 2.0 or SureCall 2.1 to SureCall 3.0 using the instructions
provided here. If you are running SureCall 1.0 or 1.1, you must first upgrade to SureCall 2.0
before upgrading to SureCall 3.0.
NOTE
Reboot your computer just prior to starting these instructions.
1 Log on to the computer where you want to install a standalone version
of SureCall 3.0. Use an account that has administrator permissions.
2 Double-click the Agilent SureCall 3.0.XX.exe file to start the
installation wizard. (See “Download the software and release notes” on
page 8 for instructions on downloading the SureCall 3.0 installation
files.)
The following message is displayed.
Figure 22
InstallAnywhere dialog box - preparing to install
The installation wizard starts.
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Figure 23
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 following message is displayed, notifying you that a version of
SureCall client already exists on the local machine.
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Figure 24
Information box – Agilent SureCall already exists
5 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 25
Alert message box
6 Click Continue to continue uninstalling SureCall.
The uninstaller program opens to the Introduction screen.
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Figure 26
2
Uninstall Agilent SureCall – Introduction screen – Windows
7 Click Uninstall to proceed.
The Uninstall Options windows opens.
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Figure 27
Uninstall Agilent SureCall – Uninstall Options screen – Windows
8 Select Uninstall specific features, and click Next.
The Choose Product Features screen opens.
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Figure 28
2
Uninstall Agilent SureCall – Choose Product Features screen – Windows
9 In the top panel, mark the Client check box. Make sure that the Server
check box is not marked.
10 Click Uninstall.
A message box opens asking you to confirm that you want to uninstall
the SureCall client.
11 Click Yes in the message box to continue uninstalling.
The SureCall client is uninstalled. When the uninstallation is complete,
the Uninstall Complete screen opens.
12 Click Done.
The uninstaller program closes and the SureCall 3.0 installation wizard
opens to the License Agreement screen. You can now continue installing
SureCall 3.0.
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Figure 29
License Agreement screen – Windows
13 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 30
2
Choose Install Set screen – Windows
14 Click the icon next to Standalone to install both the SureCall 3.0
database server and client software on this computer.
15 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 3.0 server. The
Configure Proxy Settings screen opens and you can proceed to
step 16.
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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 3.0 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 16.
Figure 31
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.
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Figure 32
2
Data Download Option screen – Windows
18 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.
NOTE
If you received an external USB drive from Agilent containing the reference and annotation
data, plug in the USB drive to your computer and enter the file path of the drive into the
Provide Data Location field.
19 Click Next.
The Choose Install Folder screen opens.
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Figure 33
Choose Install Folder screen – Windows
20 By default, the program is installed in:
C:\agilent\Agilent_SureCall_3.0.XX (where XX 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.
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.
21 Click Next.
The Choose Shortcut Folder screen opens.
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Figure 34
2
Choose Shortcut Folder screen – Windows
22 By default, program icons are installed in the Agilent SureCall program
group on your computer (where XX is the revision number). 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 3.0 on this computer, select Create Icons for All
Users. Otherwise, other users do not see the program icons.
23 Click Next.
The Pre-Installation Summary screen opens.
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Figure 35
Pre-Installation Summary screen – Windows
24 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 3.0.XX screen opens and remains open
until the installation is complete.
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Figure 36
2
Installing Agilent SureCall screen – Windows
When the SureCall installation is complete, the Install Complete screen
opens.
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Figure 37
Install Complete screen – Windows
25 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 38
2
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.
26 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 34.
Start the SureCall program, log in, and enter your license information.
See “Opening the SureCall 3.0 client software” on page 29.
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Installation of SureCall 3.0 for Windows – Software Upgrade Instructions
Upgrading SureCall on client computers
Upgrading SureCall on client computers
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.
NOTE
Before upgrading to SureCall 3.0 on computers that are only running the client software,
upgrade to SureCall 3.0 on the computer that will run the database software. See
“Upgrading a standalone version of SureCall” on page 38.
NOTE
Reboot your computer just prior to starting these instructions.
1 Double-click the Agilent SureCall 3.0.XX.exe file to start the
installation wizard.
The following message is displayed.
Figure 39
InstallAnywhere dialog box - preparing to install
The installation wizard starts.
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Figure 40
2
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 41
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 42
Alert message box
5 Click Continue to continue uninstalling SureCall.
The uninstaller program opens to the Introduction screen.
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Figure 43
2
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 3.0 installation wizard
opens to the License Agreement screen. You can now continue installing
SureCall 3.0.
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Figure 44
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 45
2
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 46
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 3.0 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.
NOTE
If incorrect database parameters are provided, or the PostgreSQL database service is not
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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2
folder, choose a shortcut location, and start the installation. For
information, see step 16 through step 25 in the section “Upgrading a
standalone version of SureCall” on page 38.
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Installation of SureCall 3.0 for Windows – Software Upgrade Instructions
Uninstalling SureCall
Uninstalling SureCall
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.
CA U T I O N
NOTE
When you completely uninstall SureCall, the database, the data contained in the database,
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.
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 47
62
Alert dialog box
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2
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 48
Uninstall Options screen – Windows
4 Select Complete Uninstall and click Next.
In the Confirmation dialog box that opens, click Yes to continue.
5 When the uninstallation is complete, a message appears. 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.
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Uninstalling SureCall
Uninstall the SureCall client software only
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 49
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.
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Figure 50
2
Uninstall Options screen – select Uninstall Specific Features – Windows
4 Select Uninstall Specific Features and click Next.
The Choose Product Features screen opens.
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Figure 51
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.
CA U T I O N
Do not select Server unless you want to remove client and server software completely,
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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Macintosh – Fresh Install Instructions
Installing Java Standard Edition (Java SE) 68
To check which versions of Java are installed 68
To install Java SE 6 68
To install Java SE 8 69
Preparing for installation 71
Installing a standalone version of SureCall 3.0 – Macintosh 74
Opening the SureCall 3.0 client software 90
Adding a SureDesign user name and password 92
Checking the data download 93
This chapter shows you how to install and get started using SureCall 3.0
on computers running the Macintosh OS X Mountain Lion or Mavericks
operating system.
For instructions on upgrading from a previous version of SureCall to
SureCall 3.0, see Chapter 4, “Installation of SureCall 3.0 for Macintosh –
Software Upgrade Instructions” on page 95.
For instructions on installing SureCall 3.0 on a Windows computer, see
Chapter 1, “Installation of SureCall 3.0 for Windows – Fresh Install
Instructions” on page 7.
Agilent Technologies
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Installation of SureCall 3.0 for Macintosh – Fresh Install Instructions
Installing Java Standard Edition (Java SE)
Installing Java Standard Edition (Java SE)
In order to install and run SureCall 3.0 on a Macintosh computer, the
computer must have Java SE 6 and Java SE 8 installed (version 6 is
needed for the SureCall installer and version 8 is needed for the SureCall
program). 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 68). If it does not have version 6 or version 8, follow the instructions
in this section to install the missing version or versions. See “To install
Java SE 6” on page 68 and “To install Java SE 8” on page 69.
To check which versions of Java are installed
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, including those for
Java. Figure 52 shows the software names for Java SE 6 and Java SE 8
as displayed on the Software System Information screen.
Figure 52
Java SE 6 and Java SE 8 installations as displayed in System Information
To install Java SE 6
If your Macintosh computer does not already have Java SE 6 installed, you
need to install it before you can install SureCall.
1 Launch an internet browser and go to the webpage:
http://support.apple.com/kb/DL1572.
2 On the right side of the screen, click Download.
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3
3 Download the Java SE 6 installer to the desired location on your
computer.
4 When download is complete, launch the Java SE 6 installer and follow
the prompts to install the software.
To install Java SE 8
If your Macintosh computer does not already have Java SE 8 installed, you
need to install it before you can install SureCall.
1 Launch an internet browser and go to the webpage:
http://www.oracle.com/technetwork/java/javase/downloads.
2 Click the Download button (Figure 53) that is above the header Java
Platform (JDK) 8u45.
Figure 53
Download button for Java Platform (JDK) 8u45
3 Under Java SE Development Kit 8u45, select Accept License
Agreement. Then, click the download link for Mac OS X x64 in the
table of products (circled in red in Figure 54).
Figure 54
Table of Java SE 8 products
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4 Download the Java SE 8 installer to the desired location on your
computer.
5 When download is complete, launch the Java SE 8 installer and follow
the prompts to install the software.
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Preparing for installation
3
Preparing for installation
Download the software and release notes
1 Go to http://www.agilent.com/genomics/surecall_soft.
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 http://www.agilent.com/genomics/surecall_soft.
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.
NOTE
You will also need to download the installer for the sequence alignment tools from the
http://www.agilent.com/genomics/surecall_soft website. See “Installing Sequence
Alignment Tools” on page 112 for instructions.
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Preparing for installation
Check system requirements before you start
Check to make sure that your computer systems meet the following
requirements. See Table 3 for minimum requirements. See Table 4 for
recommended requirements.
Table 3
Minimum requirements for running SureCall on Macintosh computers
Operating system
Macintosh OS X Mountain Lion or Macintosh OS X Mavericks
Programs
Any program that enables you to open PDF files (for example, Adobe Reader)
Java SE 6 and Java SE 8 (see “Installing Java Standard Edition (Java SE)” on page 68)
Processor
> 2.0 GHz dual-core Intel Core i5
Working memory (RAM)
Without aligners installed: 8 GB
With aligners installed: 12 GB
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
Table 4
Recommended requirements for running SureCall on Macintosh computers
Operating system
Macintosh OS X Mountain Lion or Macintosh OS X Mavericks
Programs
Any program that enables you to open PDF files (for example, Adobe Reader)
Java SE 6 and Java SE 8 (see “Installing Java Standard Edition (Java SE)” on page 68)
Processor
> 2.5 GHz dual-core Intel Core i7
Working memory (RAM)
Without aligners installed: 8 GB
With aligners installed: 16 GB
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
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Preparing for installation
3
Set up permissions for installer and users
• Make sure that the user account used to install the SureCall 3.0
software has administrator permissions on the installation computer.
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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Installing a standalone version of SureCall 3.0 – Macintosh
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 3.0 as a standalone program.
1 Log on to the computer where you want to install SureCall 3.0. 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 71. Double-click the Agilent
SureCall Edition 3.0.XX.zip folder to extract the installer.
3 Double-click the Agilent SureCall Edition 3.0.XX icon to start the
installation wizard.
The Authentication screen opens.
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Figure 55
3
Authentication screen for the installation wizard – preparing to install
4 Click directly on the lock icon near the bottom of the screen.
A dialog box opens with fields for entering a Name and Password.
5 In the dialog box, type the Name and Password for a user with
administrator rights to the computer, then click OK.
The installation wizard starts.
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Figure 56
Introduction screen for the installation wizard – Macintosh
6 Read the introductory information. Pay particular attention to the
information on RAM and hard disk space requirements.
7 Click Next.
The License Agreement screen opens.
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Figure 57
3
License Agreement screen – Macintosh
8 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 58
Choose Install Set screen – Macintosh
9 Click the icon next to Standalone to install both the database server
and client software on this computer.
10 Click Next.
The Enter Domain Properties screen opens.
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Figure 59
3
Enter Domain Properties screen – Macintosh
11 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 12.
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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NOTE
If you see a warning message titled Domain validation failed, click OK in the massage box,
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 60
Enter Administrator Details screen – Macintosh
12 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
13 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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3
If you do not want to set up new users at this time, proceed directly to
step 18 on page 82. Note that the administrator can set up new users
from within SureCall once installation is complete.
NOTE
To set up SureCall users during installation, you need to have entered the domain properties
back in step 11.
14 Click Next.
The Add SureCall Users screen opens.
Figure 61
Add SureCall Users screen – Macintosh
15 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.
16 Click Next.
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The Add SureCall Users screen advances to the step for configuring
user roles.
Figure 62
Add SureCall Users screen – Configure roles step – Macintosh
17 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.
18 Click Next.
The Configure Proxy Settings screen opens.
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Figure 63
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Configure Proxy Settings screen – Macintosh
19 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.
20 Click Next.
The Data Download Option screen opens.
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Figure 64
Data Download Option screen – Macintosh
21 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.
NOTE
If you received an external USB drive from Agilent containing the reference and annotation
data, plug in the USB drive to your computer and enter the file path of the drive into the
Provide Data Location field.
22 Click Next.
The Choose Install Folder screen opens.
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Figure 65
3
Choose Install Folder screen – Macintosh
23 By default, the program is installed in the Agilent SureCall Edition
3.0.XX folder (where XX 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.
24 Click Next.
The Choose Alias Folder screen opens.
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Figure 66
Choose Alias Folder screen – Macintosh
25 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
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Pre-Installation Summary screen – Macintosh
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 Edition 3.0.XX screen opens and remains
open until the installation is complete.
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Figure 68
Installing Agilent SureCall screen – Macintosh
When the SureCall installation is complete, the Install Complete screen
opens.
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).
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Figure 69
3
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.
NOTE
Depending on your internet connection, the download process can take anywhere from 15
minutes to 2 hours.
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 93.
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Opening the SureCall 3.0 client software
Opening the SureCall 3.0 client software
After you install the SureCall database server and client program, start
the program.
1 Double-click the SureCall 3.0 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.
After you start the program, the Login screen opens. The name and
domain for the administrator set during installation appears in the dialog
box.
Figure 70
Login screen
2 Log in with your user name and password.
3 If you need to change the domain, expand the drop-down list next to
Domain and select the correct domain.
4 Click OK.
After you log in for the first time, the Enter License dialog box opens.
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3
5 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.
6 At the bottom of the dialog box, click Browse.
The Open dialog box opens.
7 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.
8 Click OK.
The SureCall program opens.
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Adding a SureDesign user name and password
Adding a SureDesign user name and password
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 SureDesign Settings.
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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3
Checking the data download
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 27 through step 28 on
page 88.)
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.
NOTE
The source location for the files is specified on the Admin > Annotation Download screen.
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 21).
SureCall administrators can change the location from the Admin > Annotation Download
screen.
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Installation of SureCall 3.0 for
Macintosh – Software Upgrade
Instructions
Upgrading a standalone version of SureCall – Macintosh 96
Uninstalling SureCall – Macintosh 107
Uninstall the client and server software for SureCall 107
Uninstall the SureCall client software only 108
This chapter provides instructions for Macintosh users of SureCall 2.0 or
2.1 who want to upgrade to SureCall 3.0 while retaining all records
currently in their SureCall database. It also contains instructions on
uninstalling SureCall. The instructions in this chapter are specific for
Macintosh computers running the Macintosh OS X Mountain Lion
operating system.
If you want to upgrade from a previous version of SureCall to SureCall
3.0, 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 107), then follow the
instructions in Chapter 3, “Installation of SureCall 3.0 for Macintosh –
Fresh Install Instructions” on page 67.
If you want to upgrade to SureCall 3.0 from a previous version on a
Windows computer, then see Chapter 2, “Installation of SureCall 3.0 for
Windows – Software Upgrade Instructions” on page 37.
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Upgrading a standalone version of SureCall – Macintosh
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 3.0 while
retaining the data in the existing database.
NOTE
You can upgrade from SureCall 2.0 or SureCall 2.1 to SureCall 3.0 using the instructions
provided here. If you are running SureCall 1.0 or 1.1, you must first upgrade to SureCall 2.0
before upgrading to SureCall 3.0.
NOTE
Reboot your Macintosh computer just prior to starting these instructions.
1 Log on to the Macintosh computer where you want to upgrade to
SureCall 3.0. Use an account that has administrator permissions.
2 If Java Standard Edition 8 is not installed on the computer, download
and install it before proceeding with the upgrade. See “Installing Java
Standard Edition (Java SE)” on page 68 for instructions.
3 Uninstall the SureCall client software for the existing version of
SureCall. See “Uninstall the SureCall client software only” on page 108
for instructions.
4 When uninstallation of the client is complete, start the installation
program for SureCall 3.0 that you downloaded from Agilent.
5 On the Authentication screen, click the lock icon and in the dialog box
that opens, enter the Name and Password for a user with Administrator
rights to the computer.
6 Read the Introduction and then click Next.
7 Select I accept the terms of the License Agreement and then click
Next to accept the license agreement.
8 On the Choose Install Set screen opens, select Standalone.
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Figure 71
4
Choose Install Set screen – Select Standalone – Macintosh
9 Click Next.
The installation wizard looks for an existing version of SureCall server
on your computer. After finding 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 3.0 server.
The Enter Domain Properties screen opens.
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Figure 72
Enter Domain Properties screen – Macintosh
10 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 11.
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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NOTE
4
If you see a warning message titled Domain validation failed, click OK in the massage box,
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 73
Enter Administrator Details screen – Macintosh
11 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
NOTE
When upgrading from a previous version of SureCall, do not mark the Add SureCall Users
check box in the Enter Administrator Details screen. On Macintosh computers, that feature
is only available during fresh installs of SureCall 3.0.
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12 Click Next.
The Configure Proxy Settings screen opens.
Figure 74
Configure Proxy Settings screen – Macintosh
13 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.
14 Click Next.
The Data Download Option screen opens.
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Figure 75
4
Data Download Option screen – Macintosh
15 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.
NOTE
If you received an external USB drive from Agilent containing the reference and annotation
data, plug in the USB drive to your computer and enter the file path of the drive into the
Provide Data Location field.
16 Click Next.
The Choose Install Folder screen opens.
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Figure 76
Choose Install Folder screen – Macintosh
17 By default, the program is installed in the Agilent SureCall Edition
3.0.XX folder (where XX 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.
18 Click Next.
The Choose Alias Folder screen opens.
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Figure 77
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Choose Alias Folder screen – Macintosh
19 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 78
Pre-Installation Summary screen – Macintosh
20 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 3.0.XX screen opens and remains
open until the installation is complete.
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Figure 79
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Installing Agilent SureCall screen – Macintosh
When the SureCall installation is complete, the Install Complete screen
opens.
21 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 80
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.
22 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 93.
23 Start the SureCall program, log in, and enter your license information.
See “Opening the SureCall 3.0 client software” on page 90.
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4
Uninstalling SureCall – Macintosh
This section provides instructions on uninstalling the SureCall software.
On a Macintosh computer on 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 Uninstaller program for SureCall provides an easy way to remove the
SureCall client, server, and PostgreSQL programs from your computer.
CA U T I O N
When you completely uninstall SureCall, the database, the data contained in the database,
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.
1 Double-click the Uninstaller icon, located in the Uninstall Agilent SureCall XX
folder of your program folder (where XX is the version of SureCall that
you want to uninstall).
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.
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Figure 81
Uninstall Options screen – Macintosh
4 Select Complete Uninstall and click Next.
A message box opens asking you to confirm that you want to uninstall
the software.
5 In the message box, click Yes to continue.
6 When the uninstallation is complete, a message appears. 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
The Uninstaller program for SureCall provides an easy way to remove the
SureCall client program from your computer.
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4
1 Double-click the Uninstaller icon, located in the Uninstall Agilent SureCall XX
folder of your program folder (where XX is the version of SureCall that
you want to uninstall).
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 82
Uninstall Options screen – select Uninstall Specific Features – Macintosh
4 Select Uninstall Specific Features and click Next.
The Choose Product Features screen opens.
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Figure 83
Choose Product Features screen – mark Client – Macintosh
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.
CA U T I O N
Do not select Server unless you want to remove client and server software completely,
including the database, from your computer.
6 Click Uninstall.
A message box opens asking you to confirm that you want to uninstall
the client software.
7 In the message box, click Yes to continue.
8 When the uninstallation has completed, click Done.
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Installation of Sequence Alignment
Tools
Installing Sequence Alignment Tools 112
Step 1. Download the GenAligners installer from the Agilent
website 112
Step 2. Install the alignment tools on your computer 112
This chapter shows you how to install the sequence alignment tools
provided by Agilent for use with SureCall 3.0.
NOTE
If you already have the sequence alignment tools installed, verify that you have the most
recent version. If necessary, uninstall the current version before downloading and installing
the latest version.
To check the version number, open the installation folder (default installation folder is
C:\Program Files\GenAligners), then open the file version.txt.
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Installation of Sequence Alignment Tools
Installing Sequence Alignment Tools
Installing Sequence Alignment Tools
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).
NOTE
As of version 3.0, SureCall does not support alignment of Ion Torrent sequencing data.
Consequently, the GenAligners application no longer includes the TMAP aligner.
To analyze Ion Torrent data in SureCall, align the FASTQ files in Torrent Server then use the
BAM files in the SureCall analysis.
This section provides instructions for downloading and installing the
alignment tools.
NOTE
If you are upgrading the sequence alignment tools from an earlier version, uninstall the
previous version of the GenAligners application from the Windows Control Panel (or, on a
Macintosh computer, simply delete the application). If you cannot find the utility for
uninstalling, search for “uninstall a program” within the Control Panel search field. Once
the previous version has been uninstalled, download and install the latest version of the
sequence alignment tools using the instructions in this chapter.
Step 1. Download the GenAligners installer from the Agilent website
1 Go to http://www.agilent.com/genomics/surecall_soft.
2 Click Download Software.
3 Download the Sequence Aligner software (Windows or Macintosh),
saving the file to your computer.
Step 2. Install the alignment tools on your computer
1 Open the folder where you saved the GenAligners installer.
2 Double-click the GenAligners installer icon.
The GenAligners Setup wizard opens to the Welcome screen.
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Figure 84
5
GenAligners Setup - Welcome screen
3 Click Next.
The End-User License Agreement window opens.
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Figure 85
GenAligners Setup - End-User License Agreement screen
4 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 86
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GenAligners Setup - Destination Folder screen
5 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.
6 Click Next.
The Ready to Install window opens.
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Figure 87
GenAligners Setup - Ready to Install screen
7 Click Install.
The Installing GenAligners screen opens and remains open until the
installation is complete.
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Figure 88
5
GenAligners Setup - Installing GenAligners screen
When the installation is complete, the Completed the GenAligners Setup
Wizard screen opens.
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Installation of Sequence Alignment Tools
Installing Sequence Alignment Tools
Figure 89
GenAligners Setup - Completed the GenAligners Setup Wizard screen
8 Click Finish to close the wizard.
NOTE
118
Agilent recommends restarting your computer after installation of the sequence alignment
tools is complete. SureCall will automatically connect to the alignment tools when you
restart the program.
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www.agilent.com
In this book
This book gives you
instructions for installing
SureCall 3.0.
Agilent Technologies, Inc. 2015
Revision B0, June 2015
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