When you start the Galaxy server, it looks in tool_conf.xml for which tools to load. Note that functional tests use tool_conf.xml.sample, and we leave the EMBOSS tools commented out in that file, so your tool_conf.xml file will still have them commented out if you haven't changed that. Uncomment the relevant lines and the EMBOSS tools should show up. After making changes to tool_conf.xml, you'll have to restart the server.

Let us know if you have any further questions, and thanks for using Galaxy.

(Also, note that this message is more appropriate for galaxy-dev, since it's about a local installation and not our public instance, so I'm CCing that list. Feel free to subscribe at


From: "Rob Klose" <>
Date: January 14, 2011 11:04:11 AM EST
To: <>
Subject: EMBOSS

To whom it may concern.

I’m running galaxy locally on my linux machine. I noticed the web based galaxy provides a nice GUI for EMBOSS. I don’t see this tool on my local installation tools setion. I was wondering if can be installed for my local usage and how to do this.

Best wishes

Rob Klose

Date: January 14, 2011 11:04:17 AM EST
Subject: confirm fd3a7b309a2f036c4da6fb909afaad912f2fc37f

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