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. | ||
| − | * 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 |
* 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: | ||
Revision as of 12:40, 28 March 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
- 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.galaxy_0.9.4/glaunch.sh has +x attribute
- Restart BioUML server
- Galaxy analyses should appear in “Analyses” tab in the tree.
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.
- 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)
- 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()
