Hi Julien
Do you mean that you want users to only "upload" files to data libraries and use the "link to files" option instead of "copy files into galaxy"?
Can you describe your infrastructure setup so that I can provide you with a good response.
From what I understand, you have SERVER A with a galaxy install and SERVER B is your compute machine? Galaxy is submitting jobs to SERVER B for analysis/processing?
Or do you only have 1 server with Galaxy on it and it is also doing the processing?
Do you have a storage array to house the data?
Regards,
Iyad Kandalaft Bioinformatics Programmer Microbial Biodiversity Bioinformatics Science & Technology Branch Agriculture & Agri-Food Canada Iyad.Kandalaft@agr.gc.ca | (613) 759-1228
________________________________________ From: galaxy-dev-bounces@lists.bx.psu.edu [galaxy-dev-bounces@lists.bx.psu.edu] on behalf of galaxy-dev-request@lists.bx.psu.edu [galaxy-dev-request@lists.bx.psu.edu] Sent: May 27, 2014 12:00 PM To: galaxy-dev@lists.bx.psu.edu Subject: galaxy-dev Digest, Vol 95, Issue 25
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Today's Topics:
1. Re: Problem using Galaxy with a PostgreSQL database on a remote host (Dannon Baker) 2. Changes in admin menu - Upload files (Julien Daligault) 3. Re: Changes in admin menu - Upload files (Dannon Baker) 4. Re: New tool on TestToolShed still not tested (Greg Von Kuster) 5. Re: New tool on TestToolShed still not tested (Peter Cock) 6. Re: Main ToolShed wrong report: Repository does not have a test-data directory. (Greg Von Kuster) 7. Re: Installation failure on Test Tool Shed (Greg Von Kuster) 8. Re: Old Tool Shed URL http://community.g2.bx.psu.edu/ dead (Greg Von Kuster) 9. Re: ToolShed: Uploaded archives can only include regular directories and files (Greg Von Kuster) 10. Re: Old Tool Shed URL http://community.g2.bx.psu.edu/ dead (Peter Cock) 11. Re: ToolShed: Uploaded archives can only include regular directories and files (Peter Cock) 12. Re: Old Tool Shed URL http://community.g2.bx.psu.edu/ dead (Greg Von Kuster) 13. Re: Problem using Galaxy with a PostgreSQL database on a remote host (Paniagua, Eric) 14. Uploading files to galaxy from a folder (Kandalaft, Iyad) 15. complex help for conditional param (Jun Fan) 16. Re: complex help for conditional param (Peter Cock) 17. Re: Problem using Galaxy with a PostgreSQL database on a remote host (Dannon Baker) 18. Re: Problem using Galaxy with a PostgreSQL database on a remote host (Paniagua, Eric) 19. Re: Problem using Galaxy with a PostgreSQL database on a remote host (Dannon Baker)
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Message: 1 Date: Tue, 27 May 2014 07:40:13 -0400 From: Dannon Baker dannon.baker@gmail.com To: "Paniagua, Eric" epaniagu@cshl.edu Cc: "galaxy-dev@lists.bx.psu.edu" galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Problem using Galaxy with a PostgreSQL database on a remote host Message-ID: CAGn_WZn7WkihVYidHLOvL0J4cbU_xEeM02N1fKGGo8bcnYczCA@mail.gmail.com Content-Type: text/plain; charset="utf-8"
Hey Eric,
It looks like you have connection info for both tcp/ip connections and unix sockets in the connection strings. If you're logging in using "psql -h wigserv5.cshl.edu <snip>", then you only want the tcp/ip connection info. Drop the ?host=tmp off the third option you listed and I think you'll be up and running, so:
postgresql://glxeric:XXXXX@wigserv5.cshl.edu:5432/glxeric
-Dannon
On Sat, May 24, 2014 at 1:49 AM, Paniagua, Eric epaniagu@cshl.edu wrote:
Dear Galaxy Developers,
I've been banging my head against this one for a few days now.
I have two Galaxy instances. One resides on a server called "genomics", which also hosts the corresponding PostgreSQL installation. The second also resides on "genomics", but its database is hosted on "wigserv5".
Based on the tests I just ran and code I just read, sqlalchemy (not Galaxy) is ignoring the hostname/port part of the database_connection string. For reference, the connection strings I've tried are:
postgresql://glxeric:XXXXX@/glxeric?host=/tmp postgresql://glxeric:XXXXX@wigserv5.cshl.edu/glxeric?host=/tmp postgresql://glxeric:XXXXX@wigserv5.cshl.edu:5432/glxeric?host=/tmp postgresql://glxeric:XXXXX@adgdgdfdflkhjfdhfkl/glxeric?host=/tmp
All of these appear to result in Galaxy connecting to the PostgreSQL installation on genomics, as determined by Galaxy schema version discrepancies and other constraints. With each connection string, Galaxy starts up normally. I force database activity by browsing saved histories. It works every time. By all appearances, the second Galaxy instance is using the PostgreSQL database hosted on "genomics", not on "wigserv5".
All databases and roles exist, and the databases are populated.
When I comment out the "database_connection" line in universe_wsgi.ini, I get errors arising from the later configuration of PostgreSQL-specific Galaxy options, as expected.
I can connect to the database server on "wigserv5" using "psql -h wigserv5.cshl.edu -d glxeric -U glxeric" from the server "genomics".
Have you ever observed this behavior from Galaxy or sqlalchemy?
Thanks, Eric
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