MassARRAY Typer v

Transcription

1 MassARRAY Typer v MassARRAY Typer v is a maintenance update to Agena Bioscience s MassARRAY Typer v or higher application software. This version rebrands the default installation location. Software Improvements... 1 Installation Instructions... 1 Pre-Installation Requirements... 1 R Package Requirement... 1 Oracle Client Requirement... 1 ODBC requirement (for iplex Pro Sample ID Panel)... 1 Software Installation from AgenaCx.com Download... 2 Preserving Custom Columns in Plate Data View... 2 Preserving Custom Layout in Typer Analyzer 2 Installing MassARRAY Typer v Setting the License in Windows Setting the License in Windows XP... 4 Running in Windows Appendix A: Installing R Appendix B: Installing Oracle 11g... 8 Software Improvements License Manager Rebranding MassARRAY Typer v installs the License Manager in the same location on the user s PC that Typer is installed. The default location is now C:\MassARRAY instead of the old location of C:\Sequenom Installation Instructions Pre-Installation Requirements R Package Requirement MassARRAY Typer v requires R v and various R packages (RODBC, doby, gap, and RSQLite) to be installed. If R is not already installed, please follow the R installation instructions in Appendix A. Oracle Client Requirement MassARRAY Typer v requires Oracle client 11g or higher. If you have Oracle 10g client or lower, you will need to update your Oracle client. The Oracle client install instructions are available in Appendix B. To check the Oracle client version on your system, please go to Start Menu > All Programs > Oracle. You will see the Oracle version number in the Menu. ODBC requirement (for iplex Pro Sample ID Panel) If you use the iplex Pro Sample ID Panel, please note that in order for the Sample ID software to function properly, the Data Source Name for your database must match the TNS Service Name in the ODBC Data Source Administrator. If they are different, you must update the Data Source Name before running a Sample ID report. You do not need to alter the configuration if you will not be using the iplex Pro Sample ID Panel or if this has already been done when installing a previous version of MassARRAY Typer.

2 To check the ODBC configuration: 1) Go to Start Menu > All Programs > Oracle... > Configuration and Migration Tools > Microsoft ODBC Administrator. 2) Select the System DSN tab and name of your database. Examples: agenadb, sequenomdb 3) Ensure the Data Source Name and TNS Service Name are the same. A: Illustration, Newer Database Software Installation from AgenaCx.com Download Preserving Custom Columns in Plate Data View Note: This procedure is only necessary for users upgrading from MassARRAY Typer v or v who have defined custom columns in the Plate Data View in Typer Analyzer. You will need to save a copy of the file that specifies the column information before installation, and then restore it after the installation. 1) Open Windows Explorer and go to the location where Typer is installed (typically Typer 4.0/bin). 2) Make a backup copy of the ColumnInfo.xml file. 3) After installation is complete, copy your backup ColumnInfo.xml file into the new Typer 4.0/bin folder, overwriting the new one that is there. Preserving Custom Layout in Typer Analyzer B: Illustration, Older Database Note: This procedure is necessary for users who have defined a custom layout for viewing the various panes in Typer Analyzer. You will need to save a copy of the layout before installation, and then restore it after installation 1) Open Typer Analyzer and click on View > Layout > Save 2) Save your current layout as TyperLayout.cfg in the default folder, C:/Sequenom/Typer 4.0/bin. This file will be moved to the new MassARRAY folder during installation. 3) After installation is complete, restore the layout by clicking on View > Layout > Open and select the layout saved in Step 2. It will be located in the C:/MassARRAY/Typer 4.0/bin/ folder. 4) You can save this layout as your default layout, so that the panes are loaded 2

3 automatically every time, by clicking on View > Layout > Save as Default. another computer and updated the database. Click on Next to proceed. Installing MassARRAY Typer v ) Log onto the computer under an account that has administrator privileges. 2) Go to AgenaCx.com and navigate to the Typer v folder in the Product Support section. 3) Click on the Typer v Software Update link and save the file to the desktop. 4) Double-click the file that was saved to the desktop. 5) Click Next to start the installation of the software. 7) If you chose Yes to run the database scripts you will be asked to enter the database information. The default DataSource =AGENADB (newer systems) or =SEQUENOMDB (existing systems), default username =system, and default password=manager. Click on Next to proceed. 6) The following dialog allows you to change the location of your install directory and run database scripts. You will need to run the database scripts if you plan to run Sample ID reports or create 24-well plates. Select Yes to run the database scripts if this is the first computer at your site to be updated to MassARRAY Typer v or later. Choose No if your site has already installed MassARRAY Typer v or later on 3

4 8) Click Install to install the software. 2) Select the Typer-4 Product and enter the information for the license obtained from Customer Support. 3) Click Done. Running in Windows 7 The first time MassARRAY Typer is run in Windows 7, it should be started with Run as Administrator. To do this, right click on the Typer entry in the Start Menu and select Run as Administrator. Subsequently, MassARRAY Typer can be started normally. 9) Software installation will take several minutes. Click Finish to complete the installation. Setting the License in Windows 7 1) Right-click on the License Manager from the Start Menu for MassARRAY. 2) Select Run as Administrator. 3) Select the Typer-4 Product and enter the information for the license obtained from Customer Support 4) Click Done. Appendix A: Installing R ) Use the following link to obtain the R environment: 2) Click on Download R for Windows, and save the file to your computer. 3) Open the downloaded.exe file and click Run. 4) Select your language and click OK. Setting the License in Windows XP 1) Left-click on the License Manager from the Start Menu for MassARRAY. 4

5 5) Click Next to start the installation. 8) In the Select Components window, de-select the x64 Files option. 6) Click Next to accept the license. 9) Click Next to accept default startup options. 7) Click Next to accept the default installation location. 10) Click Next to confirm start menu folder. 5

6 11) Click Next to confirm additional tasks. 14) Under the Packages menu, select Install package(s). 15) Choose your location; for example, USA (CA1) and click OK. 12) Installation will start. When it is complete, click Finish. 16) Choose doby and click OK. 13) After installation is complete, four packages must be installed. Open the RGui window by double-clicking on the R icon on the desktop. 6

7 17) Under the Packages menu, choose Install packages again, choose gap, and click OK. 19) Under the Packages menu, choose Install packages again, choose RSQLite, and click OK. 18) Under the Packages menu, choose Install packages again, choose RODBC, and click OK. 20) Under the File menu, choose Exit. Click on No in the window that appears. 7

8 21) Add the path to R in the environment variables: a. Right-click on Computer and select Properties. e. Select Edit and in the Variable value field add the path to the R executable, typically C:\Program Files\R\R \bin. Note that if there is more than one path in the Variable value field, they must be separated by a semicolon. b. Select Advanced system settings. c. Select Environmental Variables d. Under System variables, select Path. f. Click OK then OK again in the Environmental Variables and System Properties windows. g. Restart computer. Appendix B: Installing Oracle 11g Note: In order to install Oracle 11g, the user must have administrative privileges on their computer. 1) Download Oracle Client Win32 Software from the MassARRAY folder in the Product Support section of AgenaCx.com. 2) Unzip/extract the downloaded file. 3) Navigate to the client folder and double-click on the setup application file. 8

9 4) Click Run. 6) Select your language and click Next. 5) Select Administrator and then click Next. 7) Change Oracle Base from C:\app\admin to C:\oracle, then click Next. 9

10 8) Click Finish. 10) Click Close when installation is finished. 9) If prompted, select Domain Networks and/or Private Networks and Allow Access. 11) You now must configure Oracle for access to the database server. Go to Start > All Programs > Oracle-OraClient11g_home1 > Configuration and Migration Tools > Net Manager. 12) Under Local, select Service Naming and then click on the + in the tool bar on the left. 10

11 13) Enter Net Service Name. Newer databases will be agenadb, older ones will be sequenomdb. Click Next. 16) Enter the Service Name (BMS) and click Next. 14) Select TCP/IP and click Next. 17) Click on Finish. 15) Enter the Host Name and Port Number (1521). The Host Name should be the same as the Net Service Name entered in step 13 (i.e., agenadb or sequenomdb). Click on Next. 11

12 18) Under the File menu, select Save Network Configuration. Then go to the File menu again and select Exit. 20) Go to the System DSN tab and click on Add. 21) Select Oracle in OraClient11g_home1 and click on Finish. 19) You now must create an ODBC entry. The ODBC is the gateway for all third-party applications, e.g., MassARRAY Typer, to access the database. For Windows 32 bit systems, navigate to Start > Control Panel > Administrative Tools and double-click on Data Sources (ODBC). For Windows 64 bit systems, navigate to C:\Windows\SysWOW64\ODBCAD32 and double-click on ODBCAD32.exe. 12

13 22) Select the TNS Service Name from the dropdown menu. This will be the name you entered earlier, either AGENADB or SEQUENOMDB. If there is a space at the end of the name, delete it. 24) Enter the Password (darwin) and click on OK. 25) Click on OK in the Testing Connection window. 23) Enter the Data Source Name (either AGENADB or SEQUENOMDB) and the User ID (charles) and click on Test Connection. 26) Click on OK to close the window. 13

14 27) Click on OK to close the window. Patents and Trademarks MassARRAY and iplex are registered trademarks of Agena Bioscience, Inc. Agena Bioscience is a trademark of Agena Bioscience, Inc. All other trademarks or service marks set forth herein are the property of their respective owners. Agena Bioscience s patented nucleic acid analysis by mass spectrometry methods and products are protected under United States patent rights including but not limited to; 6,440,705; 6,558,623; 6,730,517; 6,979,425; 6,994,969; 7,019,288; 7,025,933; 7,332,275; 7,390,672; 7,501,251; 7,888,127; 7,917,301; 8,003,317; 8,315,805; 8,349,566; 9,249,456; and 9,310,378, and patents pending including but not limited to US , and foreign counterparts including but not limited to EP B1, EP B1, EP B1, EP B1, EP B1, EP B1, and EP B1. [0217] The MassARRAY System, Typer software, and iplex Pro Sample ID Panel are For Research Use Only. Not for use in diagnostic procedures. RLN-CUS-026 R02 4/25/17 14