Galaxy

Enable Galaxy export

The following properties are set in the global.web.properties. You can override any of those in the web.properties file.

# in global.web.properties

galaxy.baseurl.default = https://usegalaxy.org

galaxy.url.value = /tool_runner?tool_id=intermine

galaxy.welcomeMessage = <b>Welcome to InterMine, 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.

galaxy.disabledMessage = Galaxy export is disabled.

Update Struts config

# webapp/src/main/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"/>

# webapp/src/main/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"/>

# webapp/src/main/resources/struts-config-model-form.xml

<form-bean name="galaxyExportForm" type="org.intermine.bio.web.struts.GalaxyExportForm"/>

Customization

Properties located in the ''global.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

# galaxy

## set to "false" to disable galaxy

galaxy.display = true

galaxy.disabledMessage = Galaxy export is disabled.

galaxy.baseurl.default = https://usegalaxy.org

galaxy.url.value = /tool_runner?tool_id=intermine

galaxy.welcomeMessage = <b>Welcome to InterMine, 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.

Export Data from InterMine to Galaxy

1. Starting from an InterMine instance, e.g. FlyMine, run a query, select the option Export -> Send to Galaxy and the data will be exported in the galaxy instance specified in the Galaxy Location field

   

2. Starting from Galaxy, use the NEW intermine tool to be redirected to the InterMine registry, select the InterMine instance you want to use to export the data, run the query, select the option Export -> Send to Galaxy and the data will be exported in the Galaxy instance you started from.

Export Identifiers from Galaxy to InterMine

Use the new InterMine interchange dataset to generate an intermediate file (tsv formatted)

and then click on View InterMine at Registry to be redirected to the InterMine registry in order to chose the InterMine instance to export the identifiers to.