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Galaxy

Enable Galaxy export

Add to ‘’web.properties’‘’ file, replacing FlyMine with your Mine name:

# in web.properties
galaxy.display = true
galaxy.disabledMessage = Galaxy export is disabled.
galaxy.baseurl.default = http://main.g2.bx.psu.edu
galaxy.url.value = /tool_runner?tool_id=flymine
galaxy.welcomeMessage = <b>Welcome to FlyMine, GALAXY users</b><br/><br/>You can run queries by clicking on the 'Templates' tab at the top of this page.&nbsp;&nbsp;You can end the query results to Galaxy from the 'EXPORT' menu in the results page.

Update Struts config

# MINE/webapp/resources/struts-config-model.xml
<action path="/galaxyExportOptions" forward="galaxyExportOptions.page"/>
<action path="/initGalaxyExportOptions"
        type="org.intermine.bio.web.struts.GalaxyExportOptionsController"/>
<action path="/galaxyExportAction" name="galaxyExportForm"
    type="org.intermine.bio.web.struts.GalaxyExportAction" parameter="method"/>
# MINE/webapp/resources/tiles-defs-model.xml
<definition name="galaxyExportOptions.page" extends="layout.template">
    <put name="body" value="galaxyExportOptions.tile"/>
<put name="pageName" value="galaxyExportOptions"/>
</definition>
<definition name="galaxyExportOptions.tile" path="/model/galaxyExportOptions.jsp"
    controllerUrl="/initGalaxyExportOptions.do"/>
# MINE/webapp/resources/struts-config-model-form.xml
<form-bean name="galaxyExportForm" type="org.intermine.bio.web.struts.GalaxyExportForm"/>

Customization

Properties located in the ‘’web.properties’‘’ file.

parameter purpose required?
display enable Galaxy export yes[1]_.
disabledMessage displayed when Galaxy export is disabled yes
baseurl.default base url of Galaxy server yes[2]_.
url.value tool runner url yes[3]_.
welcomeMessage displays on the homepage when coming from Galaxy yes
[1]when display is false
[2]default url is the main Galaxy server, but it can be replaced by any public/private server
[3]e.g. on main Galaxy server, the tool for flymine is /tool_runner?tool_id=flymine. Customize this url to specific mines, learn how to create a tool from Galaxy wiki
# galaxy
## set to "false" to disable galaxy
galaxy.display = true
galaxy.disabledMessage = Galaxy export is disabled.
galaxy.baseurl.default = http://main.g2.bx.psu.edu
galaxy.url.value = /tool_runner?tool_id=flymine
galaxy.welcomeMessage = <b>Welcome to FlyMine, GALAXY users</b><br/><br/>You can run queries by \
clicking on the 'Templates' tab at the top of this page.&nbsp;&nbsp;You can send the query results \
to Galaxy from the 'EXPORT' menu in the results page.