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 > > > > > > > > ___________________________________________________________ > > Please keep all replies on the list by using "reply all" > > in your mail client. To manage your subscriptions to this > > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ > > > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > -- The information contained in this e-mail message or any attachment(s) may be confidential and/or privileged and is intended for use only by the individual(s) to whom this message is addressed. If you are not the intended recipient, any dissemination, distribution, copying, or use is strictly prohibited. If you receive this e-mail message in error, please e-mail the sender at who...@lygos.com and destroy this message and remove the transmission from all computer directories (including e-mail servers). Please consider the environment before printing this email.
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