Download and Installation - Revision history

Smith: /* geWorkbench Installation Instructions */

2016-12-22T20:50:54Z

‎geWorkbench Installation Instructions

Smith: /* Switching between different installed JREs on Windows */

2016-12-22T20:42:49Z

‎Switching between different installed JREs on Windows

Smith: /* R installation on Windows */

2016-12-22T20:41:31Z

‎R installation on Windows

Smith: /* Installation */

2016-12-22T20:39:08Z

‎Installation

Smith: /* Running geWorkbench on Windows */

2016-12-22T20:36:20Z

‎Running geWorkbench on Windows

Smith at 20:33, 22 December 2016

2016-12-22T20:33:10Z

Smith: /* Generic - any platform */

2016-12-22T20:28:30Z

‎Generic - any platform

Smith: /* Instead you can just download a zip file */

2016-12-22T20:26:47Z

‎Instead you can just download a zip file

Smith: /* Java Environment Configuration */

2016-12-22T20:21:14Z

‎Java Environment Configuration

Smith: /* IMPORTANT Note for Windows (and Linux) */

2016-12-22T20:20:53Z

‎IMPORTANT Note for Windows (and Linux)

← Older revision		Revision as of 20:50, 22 December 2016
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−	=geWorkbench ~~Installation Instructions~~=	+	=Install and Run geWorkbench=

	==Windows (XP/Vista/7/8/10)==		==Windows (XP/Vista/7/8/10)==

← Older revision		Revision as of 20:42, 22 December 2016
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	==Switching between different installed JREs on Windows==		==Switching between different installed JREs on Windows==
−	~~The no-JRE installer versions of geWorkbench on Windows will use a system-specified version of Java, typically the highest version installed. They will ignore the JAVA_HOME environment variable.~~
−
	If you have multiple versions of Java installed, you can set JAVA_HOME to the desired version, and if you start geWorkbench simply by double-clicking on launch_geworkbench.bat, it will use the version of Java specified there.		If you have multiple versions of Java installed, you can set JAVA_HOME to the desired version, and if you start geWorkbench simply by double-clicking on launch_geworkbench.bat, it will use the version of Java specified there.

@@ Line 192: / Line 192: @@
 ==R installation on Windows==
-* '''R installation directory''' - There are specific considerations for installing R on Windows Vista/7/8.
+* '''R installation directory''' - There are specific considerations for installing R on Windows Vista/7/8/10.
 We have demonstrated two methods based on the links shown below.

@@ Line 90: / Line 90: @@
 ==Windows (XP/Vista/7/8/10)==
 ===Installation===
+Download one of the Windows installers and double-click it to begin installation, or download the Zip file version and extract geWorkbench.
-Download one of the Windows installers and double-click the installer file to begin installation, or download the Zip file version and extract it.
+New with release 2.6.0, geWorkbench installers will by default install geWorkbench to "C:\Program Files" system directory, e.g. to C:\Program Files\geWorkbench_2.6.0.  With the Zip file version, you can place the extracted folder anywhere that is convenient, either in a user directory or in e.g. C:/Program Files.
 ===Running geWorkbench on Windows===

@@ Line 96: / Line 96: @@
 ===Running geWorkbench on Windows===
-You can launch geWorkbench using the default Java max heap memory size just by using the shortcut created by the installer.  This is 2 GB for the 64-bit JVM and 950 MB for the 32-bit JVM.
+====Any 64-bit version====
 If you wish to start the 64-bit version of geWorkbench with a different (larger) memory request, you can use the launcher .bat files found in the geWorkbench installation directory, typically "C:\Program Files\geWorkbench_2.6.0".  These files are name such as "launch_geworkbench_winpc_4G.bat", and are available for starting with geWorkbench with 1, 2, 4, 8 or 16 GB of Java heap memory.

← Older revision		Revision as of 20:33, 22 December 2016
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	[http://magnet.c2b2.columbia.edu/?q=node/44&software=geWorkbench&platform=Generic&version=2.6.0 geWorkbench_v2.6.0_Generic.zip] (240,045 KB). No Java JRE is included, you must supply and configure the appropriate JRE for your machine.		[http://magnet.c2b2.columbia.edu/?q=node/44&software=geWorkbench&platform=Generic&version=2.6.0 geWorkbench_v2.6.0_Generic.zip] (240,045 KB). No Java JRE is included, you must supply and configure the appropriate JRE for your machine.
−
−	~~=geWorkbench 2.6.0 - System Requirements=~~
−	~~==Java==~~
−	* geWorkbench 2.6.0 has been developed and tested using Java 7. Versions of geWorkbench which include a built in Java 7 Runtime Environment (JRE) are provided. Using a version of geWorkbench that includes the JRE7 allows you to be sure that you are running geWorkbench in its intended environment.
−	* geWorkbench has not been extensively tested using Java 8. However, at this time there are no known incompatibilities.
−	* The "Generic" distribution of geWorkbench does not include the JRE7. Java must be installed separately. The generic distribution can be used on any machine, including Windows, Mac, Linux and others.
−	* geWorkbench can run on both 32-bit and 64-bit versions of Java on appropriate OS platforms.
−	* See the [https://www.java.com/en/download/help/sysreq.xml Java System Requirements] and [https://www.java.com/en/download/faq/java_win64bit.xml Java on 64-bit Windows] for further details.
−
−	~~==Special Java Requirements for Specific Components==~~
−	* '''GenomeSpace''' - The GenomeSpace (genomespace.org) website allows geWorkbench to be launched using a Java Web-Start application. This in turn requires a Java JRE be installed separately on your machine. The latest version of the Java 8 JRE may be used and is recommended. Either 32-bit or 64-bit versions may be used.
−
−	~~Note - Using GenomeSpace in geWorkbench does not require the use of the web start applet. It is just a convenience to start geWorkbench directly from the GenomeSpace portal.~~
−
−
−	* '''MarkUs''' - The MarkUs component molecular structure display in your web browser requires that a Java JRE be installed separately on your machine. The latest version of the Java 8 JRE may be used and is recommended. You must install the version matching your browser, e.g. 32-bit Java (i586) for 32-bit web browsers such as Firefox and Chrome on Windows. This is true even if you have a 64-bit version already installed for other reasons.
−
−
−	~~There are specific steps to configure Java for these two applets. See [[Download_and_Installation#Java_Runtime_Special_Exceptions \| Java Runtime Special Exceptions]] below.~~
−
−	~~===Obtaining Java===~~
−	* Standalone versions of Java can be downloaded from http://www.oracle.com/technetwork/java/javase/downloads.
−
−	~~==Display Driver==~~
−	* This requirement pertains only to using the PCA component 3D graph viewer.
−	* When using a 64-bit JVM, the Java 3D library requires that OpenGL version 1.2 or higher be supported by your display driver.
−
−	~~==Memory==~~
−	~~At least 4 GB is recommended. The 64-bit JRE7 version of geWorkbench 2.6.0 by default will request up to 2 GB of memory for the Java VM.~~
−
−	~~==Operating System==~~
−	* '''Windows XP/Vista/Windows 7/8/10 (32 or 64-bit)''':
−	** 32-bit versions of Windows can only run the 32-bit JRE versions of geWorkbench.
−	** 64-bit versions of Windows can run either 32-bit or 64-bit JRE versions.
−
−	* '''Mac OS X''': As geWorkbench for Mac now includes the Java JRE7, it should run on any recent version of Mac OS (Intel platform only). A previous requirement for OS X Version 10.7.3 or higher was based on using an externally installed version of Java.
−
−	* '''Linux''': no special requirements.
−
−	~~geWorkbench, unless otherwise noted for particular components, can be run on both 32 and 64-bit operating systems and JREs.~~
−
−	~~==Graphics Driver==~~
−	At least one component, the PCA viewer, uses a Java 3D library. When using a 64-bit JVM, the Java 3D library requires OpenGL version 1.2 or higher to be supported by the graphics display adapter in your computer.
−
−
−	~~==R server==~~
−	~~Several components (SAM, DeMAND, and VIPER) can use a local installation of R on your desktop computer.~~
−
−	~~This has been tested with R versions 3.1.2, 3.1.1, 3.0.3, 3.0.2 and 2.15.0.~~
−
−	~~There are special considerations for installing a local copy of R on Windows computers. Please see the section on this further below.~~
−
−	~~=IMPORTANT NOTICE ABOUT THE LICENSE=~~
−	Use of geWorkbench is governed by the rules specified in the [[geWorkbench License \| software license]]. Please make sure to read the license and understand your obligations before proceeding to download the application.


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	The forums can be viewed at https://cabig-kc.nci.nih.gov/Molecular/forums/		The forums can be viewed at https://cabig-kc.nci.nih.gov/Molecular/forums/
		+
		+
		+	=geWorkbench 2.6.0 - System Requirements=
		+	==Java==
		+	* geWorkbench 2.6.0 has been developed and tested using Java 7. Versions of geWorkbench which include a built in Java 7 Runtime Environment (JRE) are provided. Using a version of geWorkbench that includes the JRE7 allows you to be sure that you are running geWorkbench in its intended environment.
		+	* geWorkbench has not been extensively tested using Java 8. However, at this time there are no known incompatibilities.
		+	* The "Generic" distribution of geWorkbench does not include the JRE7. Java must be installed separately. The generic distribution can be used on any machine, including Windows, Mac, Linux and others.
		+	* geWorkbench can run on both 32-bit and 64-bit versions of Java on appropriate OS platforms.
		+	* See the [https://www.java.com/en/download/help/sysreq.xml Java System Requirements] and [https://www.java.com/en/download/faq/java_win64bit.xml Java on 64-bit Windows] for further details.
		+
		+	==Special Java Requirements for Specific Components==
		+	* '''GenomeSpace''' - The GenomeSpace (genomespace.org) website allows geWorkbench to be launched using a Java Web-Start application. This in turn requires a Java JRE be installed separately on your machine. The latest version of the Java 8 JRE may be used and is recommended. Either 32-bit or 64-bit versions may be used.
		+
		+	Note - Using GenomeSpace in geWorkbench does not require the use of the web start applet. It is just a convenience to start geWorkbench directly from the GenomeSpace portal.
		+
		+
		+	* '''MarkUs''' - The MarkUs component molecular structure display in your web browser requires that a Java JRE be installed separately on your machine. The latest version of the Java 8 JRE may be used and is recommended. You must install the version matching your browser, e.g. 32-bit Java (i586) for 32-bit web browsers such as Firefox and Chrome on Windows. This is true even if you have a 64-bit version already installed for other reasons.
		+
		+
		+	There are specific steps to configure Java for these two applets. See [[Download_and_Installation#Java_Runtime_Special_Exceptions \| Java Runtime Special Exceptions]] below.
		+
		+	===Obtaining Java===
		+	* Standalone versions of Java can be downloaded from http://www.oracle.com/technetwork/java/javase/downloads.
		+
		+	==Display Driver==
		+	* This requirement pertains only to using the PCA component 3D graph viewer.
		+	* When using a 64-bit JVM, the Java 3D library requires that OpenGL version 1.2 or higher be supported by your display driver.
		+
		+	==Memory==
		+	At least 4 GB is recommended. The 64-bit JRE7 version of geWorkbench 2.6.0 by default will request up to 2 GB of memory for the Java VM.
		+
		+	==Operating System==
		+	* '''Windows XP/Vista/Windows 7/8/10 (32 or 64-bit)''':
		+	** 32-bit versions of Windows can only run the 32-bit JRE versions of geWorkbench.
		+	** 64-bit versions of Windows can run either 32-bit or 64-bit JRE versions.
		+
		+	* '''Mac OS X''': As geWorkbench for Mac now includes the Java JRE7, it should run on any recent version of Mac OS (Intel platform only). A previous requirement for OS X Version 10.7.3 or higher was based on using an externally installed version of Java.
		+
		+	* '''Linux''': no special requirements.
		+
		+	geWorkbench, unless otherwise noted for particular components, can be run on both 32 and 64-bit operating systems and JREs.
		+
		+	==Graphics Driver==
		+	At least one component, the PCA viewer, uses a Java 3D library. When using a 64-bit JVM, the Java 3D library requires OpenGL version 1.2 or higher to be supported by the graphics display adapter in your computer.
		+
		+
		+	==R server==
		+	Several components (SAM, DeMAND, and VIPER) can use a local installation of R on your desktop computer.
		+
		+	This has been tested with R versions 3.1.2, 3.1.1, 3.0.3, 3.0.2 and 2.15.0.
		+
		+	There are special considerations for installing a local copy of R on Windows computers. Please see the section on this further below.
		+
		+	=IMPORTANT NOTICE ABOUT THE LICENSE=
		+	Use of geWorkbench is governed by the rules specified in the [[geWorkbench License \| software license]]. Please make sure to read the license and understand your obligations before proceeding to download the application.
		+

@@ Line 82: / Line 82: @@
 ===Generic - any platform===
-[http://magnet.c2b2.columbia.edu/?q=node/44&software=geWorkbench&platform=Generic&version=2.6.0 geWorkbench_v2.6.0_Generic.zip]  (240,045 KB).  No Java JRE is included, you must supply the appropriate JRE for your machine.
+[http://magnet.c2b2.columbia.edu/?q=node/44&software=geWorkbench&platform=Generic&version=2.6.0 geWorkbench_v2.6.0_Generic.zip]  (240,045 KB).  No Java JRE is included, you must supply and configure the appropriate JRE for your machine.
 =geWorkbench 2.6.0 - System Requirements=

@@ Line 22: / Line 22: @@
 You can avoid the installer problems by downloading the simple Zip file
-geWorkbench_v2.6.0_Windows_JRE7_x64.zip.
+geWorkbench_v2.6.0_Windows_JRE7_x64.zip
-This file contains geWorkbench2.6.0 and the 64-bit Java JRE7.
+found further below.  This file contains geWorkbench2.6.0 and the 64-bit Java JRE7.
 After unzipping the file, double-click one of the .bat files to start geWorkbench (e.g. "launch_geworkbench_winpc_4G.bat" for 4 gigabytes of Java memory), depending on how much memory you wish to request for geWorkbench.

← Older revision		Revision as of 20:21, 22 December 2016
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	If you have multiple versions of Java installed, you can set JAVA_HOME to the desired version, and if you start geWorkbench simply by double-clicking on launch_geworkbench.bat, it will use the version of Java specified there.		If you have multiple versions of Java installed, you can set JAVA_HOME to the desired version, and if you start geWorkbench simply by double-clicking on launch_geworkbench.bat, it will use the version of Java specified there.
		+
		+	==Downloading older versions of Java==
		+	Previous Java versions can be downloaded from the [http://www.oracle.com/technetwork/java/javase/archive-139210.html Java archive site]. Signing up for an Oracle web account is required.

	=Java Runtime Special Exceptions=		=Java Runtime Special Exceptions=

← Older revision		Revision as of 20:20, 22 December 2016
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	After unzipping the file, double-click one of the .bat files to start geWorkbench (e.g. "launch_geworkbench_winpc_4G.bat" for 4 gigabytes of Java memory), depending on how much memory you wish to request for geWorkbench.		After unzipping the file, double-click one of the .bat files to start geWorkbench (e.g. "launch_geworkbench_winpc_4G.bat" for 4 gigabytes of Java memory), depending on how much memory you wish to request for geWorkbench.
−
−	~~==Downloading older versions of Java==~~
−	~~Previous Java versions can be downloaded from the [http://www.oracle.com/technetwork/java/javase/archive-139210.html Java archive site]. Signing up for an Oracle web account is required.~~

	=IMPORTANT Note for Mac OS X=		=IMPORTANT Note for Mac OS X=