How to launch a GenPlay jar file - Revision history

Julien at 19:50, 24 June 2014

2014-06-24T19:50:10Z

Julien: /* Introduction */

2014-06-24T19:45:33Z

‎Introduction

Julien at 19:31, 24 June 2014

2014-06-24T19:31:14Z

Julien at 19:24, 24 June 2014

2014-06-24T19:24:39Z

Bouhassi: /* Install Java */

2014-06-24T19:19:57Z

‎Install Java

Bouhassi: /* Install Java */

2014-06-24T16:02:59Z

‎Install Java

Bouhassi: /* Install Java */

2014-06-24T15:59:37Z

‎Install Java

Julien: /* Get a GenPlay jar file */

2014-03-17T21:46:49Z

‎Get a GenPlay jar file

Nicolas: /* Introduction */

2012-08-06T20:19:22Z

‎Introduction

Nicolas at 20:13, 6 August 2012

2012-08-06T20:13:27Z

← Older revision		Revision as of 19:50, 24 June 2014
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	== Launch GenPlay using the Java WebStart technology ==		== Launch GenPlay using the Java WebStart technology ==
		+
		+	The Java WebStart is the easiest method to run GenPlay. From the [[Downloads]] page, scroll to the bottom of the page, select the version of GenPlay you want to use, set the memory you want to allocate to the software and then click on the "Launch" button.

	=== Note about Java on Windows ===		=== Note about Java on Windows ===

@@ Line 1: / Line 1: @@
 == Introduction ==
-GenPlay can be launched from the Web Start web page or downloaded as a jar file.
+Even though we recommend to fully install GenPlay using the link from the [[Downloads]] page, GenPlay can also be launched directly using Java technologies. There are two main advantages:
-There are two different ways to launch a jar file:
+- GenPlay doesn't need to be installed
-This tutorial focuses on how to launch a GenPlay jar file using the command line method. It also explains how to allocate memory to GenPlay.
+- The memory amount allocated to GenPlay can be easily adjusted
 == Requirements ==

@@ Line 7: / Line 7: @@
 This tutorial focuses on how to launch a GenPlay jar file using the command line method. It also explains how to allocate memory to GenPlay.
 == Requirements ==
@@ Line 45: / Line 44: @@
 To add GenPlay to the list of exception site, navigate to the control panel and launch the Java applet. Navigate to the security tab, click on edit site list and  add http://genplay.einstein.yu.edu to the list of site. click enter.
 == Launch GenPlay from a downloaded jar file ==
@@ Line 52: / Line 50: @@
 All GenPlay jar files are available from the [[Downloads]] page of the website.
 In this tutorial, the jar file is named "''GenPlay.jar''" and saved in a folder named "''GenPlay''".
 '''Note:''' When saving the file in Notepad change the file type as "all files" to make sure that the file you created ends in .bat.  I f you save it as a txt file, the file will be named .bat.txt and will not be recognized as a .bat file and GenPlay will not launch.
 === The command line ===
@@ Line 88: / Line 70: @@
 The second command means that GenPlay will use up to 2Gb of memory (if needed).
 '''Note:''' it is considered that Operating Systems use about 1Gb of memory. If the computer you are running GenPlay has XGb of memory, it is not advised to give more than (X-1)Gb to any Java application. If many other applications are running at the meantime, allowing too much memory to a Java application may seriously slow down your system.
+=== Launching GenPlay ===
-== Launching GenPlay ==
+==== Through the console ====
-=== Through the console ===
+===== Windows =====
 In order to type a command line, the Windows Command Prompt must be open.
@@ Line 110: / Line 90: @@
 [[File:Win_genplay_2g.png]]
-==== Linux ====
+===== Linux =====
 ''Here is how the command lines look like:''
@@ Line 119: / Line 99: @@
 [[File:Linux_genplay_2g.png]]
+==== Through a file ====
-=== Through a file ===
+===== Introduction =====
 GenPlay can also be launched using a file. It consists in writing the exact same command line in a file and save it with the right extension.
@@ Line 128: / Line 107: @@
 Why using a file? Because it will avoid you to write the command line every time! You will save time and avoid error because of typos.
-==== Windows ====
+===== Windows =====
 In Windows, you need to save the file as ".bat" file.
 Then just double-click to launch GenPlay.
-==== Linux ====
+Here is an example on how to  start GenPlay from a file on Windows computers:
 In Linux, you need to save the file as ".sh" file.
 You can run it using the "sh" command from the console or double-clicking on it from your file browser (you may have to change the execution permission).

@@ Line 10: / Line 10: @@
 == Requirements ==
-=== Install Java ===
 Java has to be installed on the computer you want to run GenPlay.
@@ Line 17: / Line 17: @@
 If more information is required, here is the official tutorial [http://www.java.com/en/download/help/download_options.xml "How do I install Java ?"].
-'''Java on Windows'''
+== Launch GenPlay using the Java WebStart technology ==
 After pressing the Launch button your browser will generally ask which application to use to Launch GenPlay.
@@ Line 35: / Line 37: @@
 If you use Java 32-bit, the maximum amount of memory you can set is about 1.4 Gb. Higher amounts of memory might cause Java to crash.
-'''Java security'''
+=== Note about Java security ===
 Since version 7 Java has augmented its security settings to prevent unsigned, uncertified software to run. GenPlay is self-signed but has not been registered to one of the major trusted Certificate Authority  because GenPlay is a free open-source software and we cannot afford the cost of the security certification.
@@ Line 45: / Line 47: @@
-'''Launch GenPlay from a downloaded jar file and controlling the amount of memory for Windows computers'''
+== Launch GenPlay from a downloaded jar file ==
 Download the jar file and save it to a folder named (for instance) GenPlay_Launch in your C: directory
@@ Line 63: / Line 70: @@
 '''Note:''' When saving the file in Notepad change the file type as "all files" to make sure that the file you created ends in .bat.  I f you save it as a txt file, the file will be named .bat.txt and will not be recognized as a .bat file and GenPlay will not launch.
-== The command line ==
+=== The command line ===
-=== Introduction ===
+==== Introduction ====
 Open a terminal (see below how to do according to your operating system) and go to the folder "''GenPlay''".
@@ Line 75: / Line 79: @@
 If the Operating System does not find the "java" variable, this [http://www.java.com/en/download/help/path.xml tutorial] will help.
-=== The Xmx parameter ===
+==== The Xmx parameter ====
 The Xmx parameter defines the maximum heap size of the Java Virtual Machine (JVM). In other terms, it defines the maximum amount of memory the java instance can use.
 Here are two examples:

@@ Line 37: / Line 37: @@
 '''Java security'''
-Since version 7 Java has augmented its security settings to prevent unsigned, uncertified software to run. GenPlay is self-signed but has not been registered to one of the major certification agency because GenPlay is a free open-source software and we cannot afford the cost of the security certification.
+Since version 7 Java has augmented its security settings to prevent unsigned, uncertified software to run. GenPlay is self-signed but has not been registered to one of the major trusted Certificate Authority  because GenPlay is a free open-source software and we cannot afford the cost of the security certification.
 To run GenPlay you must lower the Java security settings or add the GenPlay website in the list of exception sites.

@@ Line 37: / Line 37: @@
 '''Java security'''
-Since version 7 Java has augmented its security setting to prevent unsigned, uncertified software to run. GenPlay is self-signed but has not been registered to one of the major certification agency because GenPlay is a free open-source software and we cannot afford the cost of the security certification.
+Since version 7 Java has augmented its security settings to prevent unsigned, uncertified software to run. GenPlay is self-signed but has not been registered to one of the major certification agency because GenPlay is a free open-source software and we cannot afford the cost of the security certification.
-To run Genplay you must lower the security setting or add the GenPlay website in the list of exception sites.
+To run GenPlay you must lower the Java security settings or add the GenPlay website in the list of exception sites.
 To lower the Java security settings navigate to the control panel and launch the Java applet. navigate to the security tab and lower the security setting to medium.
-To add GenPlay to the list of exception site, navigate to the control panel and launch the Java applet. navigate to the security tab, click on edit site list and  add http://genplay.einstein.yu.edu to the list of site. click enter.
+To add GenPlay to the list of exception site, navigate to the control panel and launch the Java applet. Navigate to the security tab, click on edit site list and  add http://genplay.einstein.yu.edu to the list of site. click enter.
@@ Line 57: / Line 57: @@
 navigate to the GenPlay_Launch folder and click on the GenPlay_v1.0.14.bat file.
-This will launch GenPlay with 8 GB of memory.
+This will launch GenPlay with 8 Gb of memory.
 The amount of memory used by GenPlay can be changed by editing the bat file. changing the line to  -Xmx12g will launch GenPlay with 12Gb of memory

← Older revision		Revision as of 15:59, 24 June 2014
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	If more information is required, here is the official tutorial [http://www.java.com/en/download/help/download_options.xml "How do I install Java ?"].		If more information is required, here is the official tutorial [http://www.java.com/en/download/help/download_options.xml "How do I install Java ?"].
		+
		+	'''Java on Windows'''
		+	After pressing the Launch button your browser will generally ask which application to use to Launch GenPlay.
		+
		+	On most Windows computers there are two versions of Java installed, a 32-bits and a 64 bits version. We strongly recommend that you use the 64-bit version to run GenPlay because the 32-bit version is limited to 1.4Gb of RAM
		+
		+	To launch GenPlay you must point your browser to the appropriate version of Java
		+
		+	Java 64-bits is installed by default in the C:\Program Files\Java\jre7\bin directory
		+
		+	Your browser should be pointed to file javaws.exe in directory C:\Program Files\Java\jre7\bin
		+	(If you have java 6 installed the javaws.exe file is located in C:\Program Files\Java\jre6\bin
		+
		+	Java 32-bit is installed by default in the C:\Program Files (x86)\Java\jre7\bin directory
		+	Your browser should be pointed to file javaws.exe in directory C:\Program Files (x86)\Java\jre7\bin
		+	(If you have java 6 installed the javaws.exe file is located in C:\Program Files (x86)\Java\jre6\bin
		+
		+	If you use Java 32-bit, the maximum amount of memory you can set is about 1.4 Gb. Higher amounts of memory might cause Java to crash.
		+
		+	'''Java security'''
		+
		+	Since version 7 Java has augmented its security setting to prevent unsigned, uncertified software to run. GenPlay is self-signed but has not been registered to one of the major certification agency because GenPlay is a free open-source software and we cannot afford the cost of the security certification.
		+	To run Genplay you must lower the security setting or add the GenPlay website in the list of exception sites.
		+
		+	To lower the Java security settings navigate to the control panel and launch the Java applet. navigate to the security tab and lower the security setting to medium.
		+
		+	To add GenPlay to the list of exception site, navigate to the control panel and launch the Java applet. navigate to the security tab, click on edit site list and add http://genplay.einstein.yu.edu to the list of site. click enter.
		+
		+
		+	'''Launch GenPlay from a downloaded jar file and controlling the amount of memory for Windows computers'''
		+
		+	Download the jar file and save it to a folder named (for instance) GenPlay_Launch in your C: directory
		+
		+	Open Notepad and create a file containing the following line:
		+
		+	"C:\Program Files\Java\jre7\bin\java.exe" -Xmx8g -jar "C:\GenPlay_Launch\GenPlay_v1.0.14.jar"
		+
		+	Save the file with the name GenPlay_v1.0.14.bat in the folder
		+
		+	navigate to the GenPlay_Launch folder and click on the GenPlay_v1.0.14.bat file.
		+
		+	This will launch GenPlay with 8 GB of memory.
		+
		+	The amount of memory used by GenPlay can be changed by editing the bat file. changing the line to -Xmx12g will launch GenPlay with 12Gb of memory
		+
		+	'''Note:''' When saving the file in Notepad change the file type as "all files" to make sure that the file you created ends in .bat. I f you save it as a txt file, the file will be named .bat.txt and will not be recognized as a .bat file and GenPlay will not launch.

	=== Get a GenPlay jar file ===		=== Get a GenPlay jar file ===