Re: [galaxy-user] galaxy-user Digest, Vol 95, Issue 9
Actually, if the ones I ordered last year are expiring soon, I'd suggest people continue to use those before recently ordered kits. Les ----- Original Message -----
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Today's Topics:
1. Re: Urgent Question about PostgreSQL Compatibility (Paniagua, Eric) 2. Re: Urgent Question about PostgreSQL Compatibility (Dannon Baker) 3. Re: Urgent Question about PostgreSQL Compatibility (Paniagua, Eric) 4. Re: Urgent Question about PostgreSQL Compatibility (Paniagua, Eric)
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Message: 1 Date: Fri, 23 May 2014 19:49:02 +0000 From: "Paniagua, Eric" <epaniagu@cshl.edu> To: Dannon Baker <dannon.baker@gmail.com> Cc: Galaxy ?[galaxy-user@bx.psu.edu]? <galaxy-user@bx.psu.edu> Subject: Re: [galaxy-user] Urgent Question about PostgreSQL Compatibility Message-ID: <759E5BE3A1277B48ADEE4096E39269CBB22248AD@EX-HS-MBX05.cshl.edu> Content-Type: text/plain; charset="windows-1256"
Hi Dannon,
There have been some developments, and I would like to update my question accordingly.
I have set up PostgreSQL 9.1 on a separate box from our Galaxy server, and ferried the database contents over. My question is this:
What is the appropriate syntax to use for the parameter "database_connection" in universe_wsgi.ini to use a remote database server? Specifically:
Galaxy host: genomics.cshl.edu Database host: wigserv5.cshl.edu Database name: glxeric Database user/role: glxeric Database port: 5432 (postgresql default port) Database password: not required under the current configuration.
Can someone please explain how to fill in the "database_connection" parameter appropriately?
Many thanks, Eric
________________________________________ From: galaxy-user-bounces@lists.bx.psu.edu [galaxy-user-bounces@lists.bx.psu.edu] on behalf of Paniagua, Eric [epaniagu@cshl.edu] Sent: Thursday, May 22, 2014 1:38 PM To: Dannon Baker Cc: Galaxy ?[galaxy-user@bx.psu.edu]? Subject: Re: [galaxy-user] Urgent Question about PostgreSQL Compatibility
Hi Dannon,
I have attached a screenshot of the error as it appears in the Galaxy web site and a screenshot of the log.
Please let me know if I can provide any more information.
Also, please note that the version information I gave for PostgreSQL before was incorrect. I am actually running PostgreSQL 8.1.22.
Thanks for your assistance, Eric
________________________________________ From: galaxy-user-bounces@lists.bx.psu.edu [galaxy-user-bounces@lists.bx.psu.edu] on behalf of Paniagua, Eric [epaniagu@cshl.edu] Sent: Thursday, May 22, 2014 11:14 AM To: Dannon Baker Cc: Galaxy ?[galaxy-user@bx.psu.edu]? Subject: Re: [galaxy-user] Urgent Question about PostgreSQL Compatibility
Hi Dannon,
I am in a meeting right now. I should be done at noon. I'll send you more info then. Thank you for your assistance!
Best, Eric
-------- Original message -------- From: Dannon Baker Date:2014/05/22 11:08 (GMT-05:00) To: "Paniagua, Eric" Cc: "Galaxy ?[galaxy-user@bx.psu.edu]?" Subject: Re: [galaxy-user] Urgent Question about PostgreSQL Compatibility
Hey Eric,
Looking into this. Can you send the exact error/trace if available?
-Dannon
On Thu, May 22, 2014 at 10:17 AM, Paniagua, Eric <epaniagu@cshl.edu<mailto:epaniagu@cshl.edu>> wrote: Hi,
I am running a Galaxy instance at Cold Spring Harbor Laboratory, and in the process of preparing an update I have encountered some problems. When I try to create a new dataset (e.g. by running a tool), I receive an error message indicating a syntactic problem with backend database commands. Specifically, the error mentions a read-only cursor and occurs when the system is trying to look up the history hid number for the new dataset, a value which (as far as I understand it) should be an autoincrementing primary key.
My codebase is the 68a8b0397947 commit on the stable branch, plus some custom tool definitions, but no real modification to any core Galaxy code. The database I am using is PostgreSQL 9.1. I am using Python 2.6.4. In the target (production) environment, we run with 3 web server processes and 3 job runner processes, but I am encountering this error in a single-Galaxy-process test instance. The error is reported both in the logs (with a traceback originating in the bowels of SQLAlchemy) and via the web interface.
I dug through the commit history and found a comit (e1bc855165bc) with the comment "Upgrade psycopg2 to 2.5.1 (statically linked to PostgreSQL 9.2.4)." on Sep 23, 2013. I am wondering if this means I need to upgrade my database backend to PostgreSQL 2.4.x. The wrinkle lies in the fact that I need to keep 2 parallel Galaxy instances running for an extended time period (~1 month). The first is the current (not updated) local Galaxy instance, and the second is the new (updated) Galaxy instance, which naturally implies diverging databases. Does this mean I will need to maintain parallel installations of PostgreSQL 9.1 and 9.2.x? How would I go about setting up that configuration?
Any assistance on debugging this error would be greatly appreciated. Our initial goal was to roll out this update tomorrow afternoon, but that may need to be delayed because of this show-stopper. If I can provide any further useful information, please let me know, and I will be happy to do so.
Best, Eric Paniagua
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___________________________________________________________ The Galaxy User List is being replaced by the Galaxy Biostar User Support Forum at https://biostar.usegalaxy.org/
Posts to this list will be disabled in May 2014. In the meantime, you are encouraged to post all new questions to Galaxy Biostar.
For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
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To manage your subscriptions to this and other Galaxy lists, please use the interface at:
To search Galaxy mailing lists use the unified search at:
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------------------------------
Message: 2 Date: Fri, 23 May 2014 16:02:41 -0400 From: Dannon Baker <dannon.baker@gmail.com> To: "Paniagua, Eric" <epaniagu@cshl.edu> Cc: Galaxy ?[galaxy-user@bx.psu.edu]? <galaxy-user@bx.psu.edu> Subject: Re: [galaxy-user] Urgent Question about PostgreSQL Compatibility Message-ID: <CAGn_WZnY9BV9HAsMSekCDdrqUbtSGjTieRG=s75_oHxewnHrXQ@mail.gmail.com> Content-Type: text/plain; charset="utf-8"
Hey Eric,
We use sqlalchemy, and the detailed documentation is here:
http://docs.sqlalchemy.org/en/rel_0_7/core/engines.html#postgresql
That said, the basic format is: dialect+driver://username:password@host :port/database
So, you're going to be looking at something like: postgres:// glxeric@wigserv5.cshl.edu:5432/glxeric
On Fri, May 23, 2014 at 3:49 PM, Paniagua, Eric <epaniagu@cshl.edu> wrote:
Hi Dannon,
There have been some developments, and I would like to update my question accordingly.
I have set up PostgreSQL 9.1 on a separate box from our Galaxy server, and ferried the database contents over. My question is this:
What is the appropriate syntax to use for the parameter "database_connection" in universe_wsgi.ini to use a remote database server? Specifically:
Galaxy host: genomics.cshl.edu Database host: wigserv5.cshl.edu Database name: glxeric Database user/role: glxeric Database port: 5432 (postgresql default port) Database password: not required under the current configuration.
Can someone please explain how to fill in the "database_connection" parameter appropriately?
Many thanks, Eric
________________________________________ From: galaxy-user-bounces@lists.bx.psu.edu [ galaxy-user-bounces@lists.bx.psu.edu] on behalf of Paniagua, Eric [ epaniagu@cshl.edu] Sent: Thursday, May 22, 2014 1:38 PM To: Dannon Baker Cc: Galaxy ?[galaxy-user@bx.psu.edu]? Subject: Re: [galaxy-user] Urgent Question about PostgreSQL Compatibility
Hi Dannon,
I have attached a screenshot of the error as it appears in the Galaxy web site and a screenshot of the log.
Please let me know if I can provide any more information.
Also, please note that the version information I gave for PostgreSQL before was incorrect. I am actually running PostgreSQL 8.1.22.
Thanks for your assistance, Eric
________________________________________ From: galaxy-user-bounces@lists.bx.psu.edu [ galaxy-user-bounces@lists.bx.psu.edu] on behalf of Paniagua, Eric [ epaniagu@cshl.edu] Sent: Thursday, May 22, 2014 11:14 AM To: Dannon Baker Cc: Galaxy ?[galaxy-user@bx.psu.edu]? Subject: Re: [galaxy-user] Urgent Question about PostgreSQL Compatibility
Hi Dannon,
I am in a meeting right now. I should be done at noon. I'll send you more info then. Thank you for your assistance!
Best, Eric
-------- Original message -------- From: Dannon Baker Date:2014/05/22 11:08 (GMT-05:00) To: "Paniagua, Eric" Cc: "Galaxy ?[galaxy-user@bx.psu.edu]?" Subject: Re: [galaxy-user] Urgent Question about PostgreSQL Compatibility
Hey Eric,
Looking into this. Can you send the exact error/trace if available?
-Dannon
On Thu, May 22, 2014 at 10:17 AM, Paniagua, Eric <epaniagu@cshl.edu <mailto:epaniagu@cshl.edu>> wrote: Hi,
I am running a Galaxy instance at Cold Spring Harbor Laboratory, and in the process of preparing an update I have encountered some problems. When I try to create a new dataset (e.g. by running a tool), I receive an error message indicating a syntactic problem with backend database commands. Specifically, the error mentions a read-only cursor and occurs when the system is trying to look up the history hid number for the new dataset, a value which (as far as I understand it) should be an autoincrementing primary key.
My codebase is the 68a8b0397947 commit on the stable branch, plus some custom tool definitions, but no real modification to any core Galaxy code. The database I am using is PostgreSQL 9.1. I am using Python 2.6.4. In the target (production) environment, we run with 3 web server processes and 3 job runner processes, but I am encountering this error in a single-Galaxy-process test instance. The error is reported both in the logs (with a traceback originating in the bowels of SQLAlchemy) and via the web interface.
I dug through the commit history and found a comit (e1bc855165bc) with the comment "Upgrade psycopg2 to 2.5.1 (statically linked to PostgreSQL 9.2.4)." on Sep 23, 2013. I am wondering if this means I need to upgrade my database backend to PostgreSQL 2.4.x. The wrinkle lies in the fact that I need to keep 2 parallel Galaxy instances running for an extended time period (~1 month). The first is the current (not updated) local Galaxy instance, and the second is the new (updated) Galaxy instance, which naturally implies diverging databases. Does this mean I will need to maintain parallel installations of PostgreSQL 9.1 and 9.2.x? How would I go about setting up that configuration?
Any assistance on debugging this error would be greatly appreciated. Our initial goal was to roll out this update tomorrow afternoon, but that may need to be delayed because of this show-stopper. If I can provide any further useful information, please let me know, and I will be happy to do so.
Best, Eric Paniagua
___________________________________________________________ The Galaxy User List is being replaced by the Galaxy Biostar User Support Forum at https://biostar.usegalaxy.org/
Posts to this list will be disabled in May 2014. In the meantime, you are encouraged to post all new questions to Galaxy Biostar.
For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
___________________________________________________________ The Galaxy User List is being replaced by the Galaxy Biostar User Support Forum at https://biostar.usegalaxy.org/
Posts to this list will be disabled in May 2014. In the meantime, you are encouraged to post all new questions to Galaxy Biostar.
For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
To search Galaxy mailing lists use the unified search at:
Hello Les, Am assuming this was an accidental post. If you have a question, please post it as a new topic on the /_Galaxy Biostar _/ <https://biostar.usegalaxy.org/>forum. This mailing list has been retired and will be closing completely soon (also, posting replies to digest threads is discouraged). How to get started with Galaxy Biostar: https://wiki.galaxyproject.org/Support/Biostar Best, Jen Galaxy team On 5/24/14 6:41 PM, Les Dethlefsen wrote:
Actually, if the ones I ordered last year are expiring soon, I'd suggest people continue to use those before recently ordered kits.
Les
-- Jennifer Hillman-Jackson http://galaxyproject.org
participants (2)
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Jennifer Jackson -
Les Dethlefsen