Installing GenePattern

Upgrading: If you are upgrading an existing GenePattern installation, read FAQ 2.2. It contains critical information on preserving GenePattern settings and data. View FAQ 2.2.

Start Installation

▶To begin installing GenePattern, click here to display the software download page:


The instructions show screens as they appear on Windows.
On other platforms, they may look slightly different.
▶Click the Download link for your platform and save the file to your hard drive. To start the installation:

• On Windows, double-click on the downloaded GPServer.exe file.
  Note: You must be logged on as an administrator to install software on Windows.
• On Mac, double-click the downloaded GPServer.zip file. After expanding the zip file, double-click GPserver.
• On Linux, open a shell, cd to the directory where you downloaded the installer, and at the prompt type:
  sh ./GPserver.bin
• On other Java-enabled platforms, double-click on the downloaded GPServer.exe file.

The installer will be downloaded to your machine and launched. While the installer is launching, you will see the following screen:



When the installer finishes launching, you will see the following screen. InstallAnywhere will guide you through the installation of the GenePattern Server.



▶Click Next to begin the installation.

Install R (Linux only)

On Linux, you will see a screen prompting you to install R from the R website.



▶Install R, then click Next.

Note: On platforms other than Linux, the GenePattern installer installs R for you.

License Agreements

You will see license agreements for software packages required by GenePattern.

• On Windows, you will see license agreement screens for Apache Tomcat, ActiveState Perl, and R.
• On Mac, you will see license agreement screens for Apache Tomcat and R.
• On Linux, you will see a license agreement screen for Apache Tomcat.
• On other Java-enabled platforms, you will see license agreement screens for Apache Tomcat, ActiveState Perl, and R.

▶For each license agreement, review the license. Then select I accept the terms of the License Agreement and click Next.

Install R (Mac only)

On Mac, you will see a screen that shows where GenePattern installs R:



▶Click Next to continue.

Choose Install Folder

You will be prompted to choose the directory where the GenePattern server will be installed.



▶When you have selected the install folder, click Next.

Choose Folder for Server Icons

You will see the following screen, allowing you to select the location for the GenePattern server icons.

• On Windows, this screen is labeled Choose Shortcut Folder.
• On Mac, this screen is labeled Choose Alias Folder.
• On Linux, this screen is labeled Choose Link Folder.
• On other Java-enabled platforms, this screen is labeled Choose Shortcut Folder.

▶Select your preferred location for the GenePattern Server icons and click Next.

You will see the following screen, prompting you to set the default settings for the GenePattern Server.
You can scroll to access all of them.



The settings are as follows:

email address to notify for problems	Email address of the technical contact for the server. If the GenePattern server encounters severe problems, it will send a message to this address.
# days to hold data before purging	The GenePattern server will delete results files older than this number of days.
time of day to run job purge	Time of day when old result files will be deleted.
webserver port	Port used by the GenePattern server. Change this only if you have another process running on port 8080.
HSQL port	Port used by GenePattern's database. Change this only if you have another process running on port 9001.
R 2.5	Home directory for Release 2.5 of R: On Windows and other Java-enabled platforms this is the directory in which R will be installed. On Mac, this option is omitted. GenePattern installs R 2.5 in the /Library/Frameworks/R.framework/Versions/2.5 directory. On Linux, enter the pathname to your R 2.5 home directory.
Perl	Home directory for Perl: On Windows, this is the directory in which Perl will be installed. On Mac, this directory is ignored. On Linux, enter the pathname to your Perl home directory. On other Java-enabled platforms, this is the directory in which Perl will be installed.

▶After making any necessary changes, click Next.

Web Proxy

You will see a pop-up window asking you if you use a web proxy to connect to sites outside your network.



If you aren't certain whether you use a proxy or not, click No. You can change this setting later, as described in the GenePattern Web Client Guide.

If you do use a proxy, click Yes. You will see the following screen where you can enter your configuration details.



When you are done, click Next.

Confirm LSID Authority

You will see a screen confirming your LSID Authority.



This string of characters will transparently and unambiguously identify elements of your GenePattern server. You will not need to remember this setting! You do need to ensure that this setting is unique for each installation of the GenePattern server. In almost every installation the default format will accomplish this. The default format is 8080.<your user name and machine name>.<your domain name>.

▶If your organization has not defined an LSID authority, click Next.
If your organization has an LSID authority, enter it in place of the domain name, then click Next.

You will see a summary of the settings you have chosen.



▶Click Previous to change any of these settings or Install to begin the installation.

When the installation completes, you will see the following screen:



▶Click Done.

When the installation completes, the GenePattern server will launch automatically. If it does not, you can launch the server by double-clicking the Start GenePattern Server icon. This icon will be located where you chose to install it in the "Choose Folder for Server Icons" step.

On Windows, while the server is starting, the cursor displays as an hourglass. The server is ready when the cursor returns to normal.

On Mac, while the server is starting, the server icon bounces in the Dock. The server is ready when the icon stops bouncing.



On Linux, if you launch into a terminal window, you will see several messages. When the ready message appears, the server is running.

On other Java-enabled platforms, when the server launches, you will see a console window appear on your screen. As on Linux, the console window will display several messages. When the ready message appears, the server is running.

Register

The first time the GenePattern server is launched, the GenePattern Registration page will appear in your browser. Fill out the registration form, read the license agreement, and click the I Agree button at the bottom of the form.

When you have completed and submitted the registration form, the GenePattern Configuration page appears, as shown below. You are now ready to configure your GenePattern server. The 5 required steps are listed on the left-hand side of the GenePattern Configuration page.

View Server Installation Report

In the right-hand side of the GenePattern Configuration page, you will see a report summarizing the installation results.



If your summary contains errors other than those described below, there may have been problems with the installation. Please contact gp-help@broadinstitute.org.

• On Linux, if R is not installed you will see the following errors:
  WARNING - There was a problem copying /usr/lib/R/library/GenePattern
  WARNING - Therre was a problm moving /usr/lib/R/library/GenePattern/runVisualizer.jar
  WARNING - Shortcut [for R] has no target
  ERROR - Unable to locate ASCII text file [for R] to be manipulated. Deferring...

Install Modules

▶Click the Install modules link. You will see the screen below, which lists the modules that are available.

▶Click Install Checked and all the available modules will be installed.




As each module is installed, a check mark appears in the far right column.



If a module requires additional software, you will be prompted to install the necessary software. For example, a number of modules require the MATLAB runtime component.

When a check mark appears next to the last module in the list, all of the modules have been installed.

Download Sample Datasets

Return to the GenePattern Configuration Page and click on the Download sample datasets link. You will see the screen shown below, providing links to sample datasets used in the GenePattern tutorial. To download a dataset, click on its link.

Log in to the GenePattern Server

▶Click the Login and begin using GenePattern link.

You will see the home page of the GenePattern Web Client:



You are now ready to use GenePattern. To learn more, view the Quick Start (10 minutes) or the Tutorial (40 minutes).

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