Difference between revisions of "Galaxy installation"
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| − | 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: | ||
| + | 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 | ||
| + | |||
| + | * Create and change ownership of .python-eggs folder usually located in tomcat home: | ||
| + | mkdir /usr/share/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: | * Visit $SERVER_PATH/analyses. There should be “Galaxy” folder with “default.config” file (create it if absent). The file content should be the following: | ||
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* Replace $GALAXY_DIST with your path and optionally change galaxy.tmp | * Replace $GALAXY_DIST with your path and optionally change galaxy.tmp | ||
| − | * Make sure that $SERVER_PATH/plugins/ru.biosoft. | + | * Make sure that $SERVER_PATH/plugins/ru.biosoft.workbench_{{BioUML current version}}/glaunch.sh has +x attribute |
* Restart BioUML server | * Restart BioUML server | ||
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* 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. | * 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. | ||
| − | * | + | * If you want to create your own tools, refer to [[Creating Galaxy tool]] page. |
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[[Category:Installation]] | [[Category:Installation]] | ||
| + | [[Category:Galaxy]] | ||
Latest revision as of 11:31, 30 July 2013
This page describes how to integrate Galaxy with installed BioUML server.
- 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
- Create and change ownership of .python-eggs folder usually located in tomcat home:
mkdir /usr/share/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:
name = Galaxy class = ru.biosoft.galaxy.GalaxyDataCollection plugins=ru.biosoft.galaxy galaxy.path = $GALAXY_DIST galaxy.tmp = /tmp
- Replace $GALAXY_DIST with your path and optionally change galaxy.tmp
- Make sure that $SERVER_PATH/plugins/ru.biosoft.workbench_2023.3/glaunch.sh has +x attribute
- Restart BioUML server
- Galaxy analyses should appear in “Analyses” tab in the tree.
[edit] Notes
- 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.
- If you want to create your own tools, refer to Creating Galaxy tool page.
