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
___________________________________________________________ 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 wholtz@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. ___________________________________________________________ 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/