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 <who...@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 <jmchil...@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 <bgra...@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 <bgra...@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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