Julien,

You have a couple of options. Maybe the file you are interested in is the upload tool, which can control if uploads get rejected or not. This is in tools/data_source/upload.py & .xml

However, the file you are looking for is ./templates/webapps/galaxy/library/common/common.mako <-- this provides the drop down menu that you want to modify

<div class="form-row"> <label>Upload option:</label> <div class="form-row-input"> ${upload_option_select_list.get_html()} </div> <div class="toolParamHelp" style="clear: both;"> Choose upload option (file, directory, filesystem paths, current history). </div> <div style="clear: both"></div> </div>

It seems to call upload_option_select_list.get_html() to get the list, which is defined in lib/galaxy/webapps/galaxy/controllers/library_common.py

Hope that helps get you started.

Regards,

Iyad Kandalaft Bioinformatics Programmer Microbial Biodiversity Bioinformatics Science & Technology Branch Agriculture & Agri-Food Canada Iyad.Kandalaft@agr.gc.ca | (613) 759-1228 ________________________________ From: Julien Daligault [daligault@ijm.univ-paris-diderot.fr] Sent: May 28, 2014 10:29 AM To: Kandalaft, Iyad Subject: Re: [galaxy-dev] Changes in admin menu - Upload files

Hi Iyad,

We have a SERVER A composed of computing machine with galaxy instances and a storage machine where data are upload. Galaxy instance are proposed on virtual machine, so each team of our institute have is own galaxy instance. To be sure that people upload data on the storage machine and then create a link by filesystem path in galaxy (and not upload directly data on galaxy, so on computing machine), I want that upload option "Upload files from filesystem paths" appears directly when we use Manage data librarieshttps://integraseq.mti.univ-paris-diderot.fr/galaxy60/library_admin/browse_libraries in the Admin menu.

I tried to change "home/galaxy/lib/galaxy/webapps/galaxy/controllers/library_common.py" and "/home/galaxy/lib/galaxy/model/__init__.py" to do that but it is not evident "Upload files" option appears always in first. I just arrived to put "Link to files without copying into Galaxy in first in the Copy data into Galaxy? option by changing "/home/galaxy/templates/library/common/common.mako" file.

If you have a solution, it will be wonderful

Regards,

Julien

Julien Daligault Plateforme Génomique-Transcriptomique (583B) INSTITUT JACQUES MONOD CNRS-Université Paris Diderot Bât. Buffon - 15 rue Hélène Brion 75205 Paris Cedex 13 - France tel : +33 1 57 27 81 31 daligault@ijm.univ-paris-diderot.frmailto:daligault@ijm.univ-paris-diderot.fr

On 05/28/2014 03:54 PM, Kandalaft, Iyad wrote:

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.camailto:Iyad.Kandalaft@agr.gc.ca | (613) 759-1228

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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.commailto:dannon.baker@gmail.com To: "Paniagua, Eric" epaniagu@cshl.edumailto:epaniagu@cshl.edu Cc: "galaxy-dev@lists.bx.psu.edu"mailto:galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edumailto: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.commailto: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/glxericmailto:postgresql://glxeric:XXXXX@wigserv5.cshl.edu:5432/glxeric

-Dannon

On Sat, May 24, 2014 at 1:49 AM, Paniagua, Eric epaniagu@cshl.edumailto: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=/tmpmailto:postgresql://glxeric:XXXXX@wigserv5.cshl.edu/glxeric?host=/tmp postgresql://glxeric:XXXXX@wigserv5.cshl.edu:5432/glxeric?host=/tmpmailto: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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