Re: [galaxy-dev] Problem with cleaning up galaxy datasets
repost bounced msg, see why below --------- Date: Sat, 14 Apr 2012 22:33:22 +0200 From: Klaus Metzeler <mail@klaus-metzeler.de> To: Michael Moore <michaelglennmoore@gmail.com> Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Problem with cleaning up galaxy datasets Message-ID: <4F89DF12.6010606@klaus-metzeler.de> Content-Type: text/plain; charset=ISO-8859-1; format=flowed OK, this pointed me to the right direction. The universe_wsgi.ini file has a key that reads: database_connection = sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE This entry was commented out in my version of the file (ie, had a # in front of it). While Galaxy itself uses this database connection by default, but the cleanup script looks for this config file entry to locate the database. So, if anyone encounters the same problem, just un-comment this entry and all runs fine. Thanks for your help, Michael. -- Why did this bounce? Digest content not stripped (#2). If you reply to a thread in a digest, please 1. Change the subject of your response from "Galaxy-dev Digest Vol ..." to the original subject for the thread. 2. Strip out everything else in the digest that is not part of the thread you are responding to. Thanks Klaus for sending in the solution! - Galaxy team -- Jennifer Jackson http://galaxyproject.org
Dear all, I have done what was suggested in this thread (remove the # sign), but somehow I still got the same error. Any suggestions on how to get past this? Cheers, Diana On Mon, Apr 16, 2012 at 12:51 AM, Jennifer Jackson <jen@bx.psu.edu> wrote:
repost bounced msg, see why below
--------- Date: Sat, 14 Apr 2012 22:33:22 +0200 From: Klaus Metzeler <mail@klaus-metzeler.de> To: Michael Moore <michaelglennmoore@gmail.com> Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Problem with cleaning up galaxy datasets Message-ID: <4F89DF12.6010606@klaus-**metzeler.de<4F89DF12.6010606@klaus-metzeler.de>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
OK, this pointed me to the right direction. The universe_wsgi.ini file has a key that reads:
database_connection = sqlite:///./database/universe.**sqlite?isolation_level=**IMMEDIATE
This entry was commented out in my version of the file (ie, had a # in front of it). While Galaxy itself uses this database connection by default, but the cleanup script looks for this config file entry to locate the database. So, if anyone encounters the same problem, just un-comment this entry and all runs fine.
Thanks for your help, Michael. --
Why did this bounce? Digest content not stripped (#2). If you reply to a thread in a digest, please 1. Change the subject of your response from "Galaxy-dev Digest Vol ..." to the original subject for the thread. 2. Strip out everything else in the digest that is not part of the thread you are responding to.
Thanks Klaus for sending in the solution!
- Galaxy team
--
Jennifer Jackson http://galaxyproject.org
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diana michelle magbanua -
Jennifer Jackson