Hi Scott,

I've recently hit the exact same problem. Have you had any success since then with resolving this? I did some poking around and made a bit of progress, but still no solution.

The Data Manager page under Run Data Manager Tools contains URLs like this:

https://galaxy.example.com/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_fetch_genome_dbkeys_all_fasta%2Fdata_manager_fetch_genome_all_fasta_dbkey%2F0.0.1

Loading that URL results in an attempted load of:

https://galaxy.example.com/api/tools/toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_fetch_genome_dbkeys_all_fasta%2Fdata_manager_fetch_genome_all_fasta_dbkey%2F0.0.1/build?

Which results in a 404 error. I believe the escaping of the slashes is accidental, as the they are in the path and not in parameters. Changing the %2F to / as shown here: 

https://galaxy.example.com/api/tools/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_dbkeys_all_fasta/data_manager_fetch_genome_all_fasta_dbkey/0.0.1/build?

results in the URL being found and you get back a bunch of JSON about the tool. I tried looking in the Galaxy code to see if I could quickly determine where the /root controller is, but I wasn't successful. Perhaps this is now enough information that one of the developers might be able to help us.

-Will

On Mon, Apr 11, 2016 at 9:55 AM, Scott Szakonyi <Scott.B.Szakonyi.1@nd.edu> wrote:
Hello,

I'm having an odd problem after updating to the latest version of Galaxy. My users prepare data for analysis using data manager tools, such as "data_manager_bwa_mem_index_builder". When an attempt is made to run one of these tools, a pop up window opens stating "Tool request failed" and underneath "Uncaught error". I've pored over all the Galaxy system logs and can't find anything that might indicate what is happening. I've uninstalled and reinstalled the data manager tools, restarted both the Galaxy service and the server, to no avail. I get this same error with any installed data manager, yet all the standard tools are executing correctly and don't seem to be having any issues.

If anyone can offer some insight or suggestions for resolving this issue, I'd be most appreciative.

Best regards,

--
Scott B. Szakonyi
Research Programmer

Center for Research Computing
107 Information Technology Center
Notre Dame, IN 46556
http://crc.nd.edu

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