Galaxy installation - Revision history

Lan@dote.ru: glaunch location

2013-07-30T04:31:48Z

glaunch location

2013-06-19T10:41:01Z

2013-06-19T10:40:44Z

2013-04-19T05:42:28Z

2013-04-19T05:36:01Z

2013-04-18T07:29:22Z

2013-04-18T07:28:27Z

2013-04-18T07:22:17Z

2013-03-28T05:40:45Z

2013-03-28T05:33:24Z

@@ Line 24: / Line 24: @@
 * Replace $GALAXY_DIST with your path and optionally change galaxy.tmp
-* Make sure that $SERVER_PATH/plugins/ru.biosoft.galaxy_0.9.4/glaunch.sh has +x attribute
+* Make sure that $SERVER_PATH/plugins/ru.biosoft.workbench_{{BioUML current version}}/glaunch.sh has +x attribute
 * Restart BioUML server

@@ Line 13: / Line 13: @@
 * Create and change ownership of .python-eggs folder usually located in tomcat home:
    mkdir /usr/share/tomcat6/.python-eggs
-   chown -R tomcat6:tomcat6 .python-eggs
+   chown -R tomcat6:tomcat6 /usr/share/tomcat6/.python-eggs
 * Visit $SERVER_PATH/analyses. There should be “Galaxy” folder with “default.config” file (create it if absent). The file content should be the following:

@@ Line 10: / Line 10: @@
 * Change ownership of $GALAXY_DIST folder:
    chown -R tomcat6:tomcat6 $GALAXY_DIST
 * Visit $SERVER_PATH/analyses. There should be “Galaxy” folder with “default.config” file (create it if absent). The file content should be the following:

@@ Line 1: / Line 1: @@
-This page describes how to integrate Galaxy with installed BioUML server.
+This page describes how to integrate {{Galaxy}} with installed BioUML server.
-* [http://galaxyproject.org/ Download Galaxy distribution] and unpack it somewhere. It usually contains galaxy_dist directory. Let’s say it’s $GALAXY_DIST
+* [http://wiki.galaxyproject.org/Admin/Get%20Galaxy/ Download Galaxy distribution] and unpack it somewhere. It usually contains galaxy_dist directory. Let’s say it’s $GALAXY_DIST
 * Galaxy requires python eggs, starting galaxy server for the first time will acquire these dependencies. Run the following command from $GALAXY_DIST folder:
@@ Line 29: / Line 29: @@
 * Note that only some Galaxy tools work “out-of-the-box”. For many of them additional software or data files (like genome indexes, etc.) must be installed and properly configured.
-* List of available Galaxy tools is in $GALAXY_DIST/tool_conf.xml. Tool files are located inside $GALAXY_DIST/tools directory. So you may try to create your own tools there (or disable existing ones)
+* If you want to create your own tools, refer to [[Creating Galaxy tool]] page.
-−
-* To reload Galaxy configuration (after you changed tool_conf.xml or xml-files of specific tools) you should log in to BioUML as administrator select “Script” tab (in right-bottom set of tabs) and type there the following command:
- galaxy.reload()
 [[Category:Installation]]

@@ Line 6: / Line 6: @@
    sh run.sh
-  After successful setup it will write "Starting server in PID", kill galaxy server with Ctrl^C.
+After successful setup it will write "Starting server in PID", kill galaxy server with Ctrl^C.
 * Change ownership of $GALAXY_DIST folder:

← Older revision		Revision as of 07:22, 18 April 2013
Line 2:		Line 2:

	* [http://galaxyproject.org/ Download Galaxy distribution] and unpack it somewhere. It usually contains galaxy_dist directory. Let’s say it’s $GALAXY_DIST		* [http://galaxyproject.org/ Download Galaxy distribution] and unpack it somewhere. It usually contains galaxy_dist directory. Let’s say it’s $GALAXY_DIST
		+
		+	* Galaxy requires python eggs, starting galaxy server for the first time will acquire these dependencies. Run the following command from $GALAXY_DIST folder:
		+	sh run.sh
		+	After successful setup it will write "Starting server in PID", kill galaxy server with Ctrl^C.
		+
		+	* Change ownership of $GALAXY_DIST folder:
		+	chown -R tomcat6:tomcat6 $GALAXY_DIST

	* Visit $SERVER_PATH/analyses. There should be “Galaxy” folder with “default.config” file (create it if absent). The file content should be the following:		* Visit $SERVER_PATH/analyses. There should be “Galaxy” folder with “default.config” file (create it if absent). The file content should be the following:

← Older revision		Revision as of 05:33, 28 March 2013
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	* To reload Galaxy configuration (after you changed tool_conf.xml or xml-files of specific tools) you should log in to BioUML as administrator select “Script” tab (in right-bottom set of tabs) and type there the following command:		* To reload Galaxy configuration (after you changed tool_conf.xml or xml-files of specific tools) you should log in to BioUML as administrator select “Script” tab (in right-bottom set of tabs) and type there the following command:
	galaxy.reload()		galaxy.reload()
		+
		+	[[Category:Installation]]