Hi Bruno,

You may be able to get it to work if you directly specify the tool_shed.ini file that you want to use and also provide the entire toolshed url including protocol, e.g:

TOOL_SHED_CONFIG_FILE=path/to/tool_shed.ini sh run_tool_shed.sh -bootstrap_from_tool_shed https://testtoolshed.g2.bx.psu.edu

It does seem as though there is an issue with the automatic resolution of which ini file to use, probably due to the recent /config/ changes.

Hope that helps,

Dan

On Nov 13, 2014, at 12:35 PM, Will Holtz <wholtz@lygos.com> wrote:

I successfully did the tool shed bootstrapping with postgresql once. But beyond that, I don't think I can offer much advice.

-Will

On Thu, Nov 13, 2014 at 7:41 AM, John Chilton <jmchilton@gmail.com> wrote:

Hey Bruno,

  So Greg has moved on new exciting things and I am not sure if there
is anyone who now routinely does the tool shed bootstrapping workflow
that can help.

  I tried the bootstrapping process and it worked fine with an sqlite
database - maybe it is not compatible with postgres? Want to try
sqlite instead - should be fine for testing?

-John

On Mon, Nov 10, 2014 at 3:42 PM, Bruno Grande <bgrande@sfu.ca> wrote:
> I had the brilliant idea of sending the previous email out on a Friday
> afternoon/evening. I'm just following up with this thread.
>
> Best regards,
> Bruno
>
> ----------
> Bruno Grande, B.Sc. (Hons)
> M.Sc. Candidate
> Dr. Ryan Morin's Laboratory
> Molecular Biology and Biochemistry, Simon Fraser University
> SSB7133, 8888 University Drive, Burnaby, BC, Canada, V5A 1S6
>
> On Fri, Nov 7, 2014 at 2:17 PM, Bruno Grande <bgrande@sfu.ca> wrote:
>>
>> I'm setting up a local development Tool Shed according to Greg Von
>> Kuster's blog post. During the bootstrapping process, it seems that the
>> creation of the admin user based on the information in user_info.xml fails
>> because of a SQLAlchemy error (see attached stdout.txt). As a result, I
>> believe the API calls for creating categories and users also fail, because
>> they depend on the existence of admin user.
>>
>> This error seems to be due to a missing repository table in the database.
>> I ran the SQL query against the Tool Shed database within PostgreSQL after
>> the failed bootstrapping command and it returned no error, because the
>> repository table actually exists.
>>
>> So, I don't know whether the SQL query is being run against the wrong
>> database (e.g. the Galaxy database) or if the database schema isn't properly
>> set up by the time SQLAlchemy attempts the query.
>>
>> I'm using the latest version of Galaxy (revision 83f821c5ecc1).
>>
>> Best regards,
>> Bruno
>
>
>

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