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(a)agr.gc.ca | (613) 759-1228
________________________________
From: Julien Daligault [daligault(a)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
libraries<https://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.fr<mailto: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.ca<mailto: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)
----------------------------------------------------------------------
Message: 1
Date: Tue, 27 May 2014 07:40:13 -0400
From: Dannon Baker <dannon.baker@gmail.com><mailto:dannon.baker@gmail.com>
To: "Paniagua, Eric" <epaniagu@cshl.edu><mailto:epaniagu@cshl.edu>
Cc: "galaxy-dev@lists.bx.psu.edu"<mailto:galaxy-dev@lists.bx.psu.edu>
<galaxy-dev@lists.bx.psu.edu><mailto: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><mailto: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<mailto:postgresql://glxeric:XXXXX@wigserv5.cshl.edu:5432/glxeric>
-Dannon
On Sat, May 24, 2014 at 1:49 AM, Paniagua, Eric
<epaniagu@cshl.edu><mailto: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<mailto:postgresql://glxeric:XXXXX@wigserv5.cshl.edu/glxeric?host=/tmp>
postgresql://glxeric:XXXXX@wigserv5.cshl.edu:5432/glxeric?host=/tmp<mailto: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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