Ilya, you can use trans.request.host to get the base url.
On Oct 20, 2011, at 11:52 AM, Chorny, Ilya wrote:
I thought I would add this to the list in case anyone in the galaxy :) knew
the answer. I get a mapping error every time I invoke url_for. What variable
stores the base url for the
Joseph Hargitai wrote:
Hi,
i was browsing through the list and found many entries for this issue but not
a definite answer.
We are actually running into this error for simple file uploads from the
internal filesystem.
Hi Joe,
This error occurs when the job's standard output and
Nate,
this error is intermittent. You resubmit the same job twice or three time and
then it works. Once we are over the midterm exams - which use galaxy - we will
try to switch the filesystem from autofs to hard mount. We suspect this to be
the issue.
Could we suppress e and o SGE style
I need the base_url and the proxy. That is why I am using cookie_path. Any
thoughts on how to get both.
Thanks,
Ilya
-Original Message-
From: Greg Von Kuster [mailto:g...@bx.psu.edu]
Sent: Friday, October 21, 2011 6:11 AM
To: Chorny, Ilya
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re:
Thanks Greg,
I created the database instance and set the path at universe_wsgi.ini.
Then when I run sh run.sh I get the following error message:
root@aedes:/home/koala2/galaxy-dist# sh run.sh
python path is:
/home/koala2/galaxy-dist/eggs/numpy-1.6.0-py2.7-linux-x86_64-ucs4.egg,
Also, I do not have access to trans in the Tools class in
lib/galaxy/tools/__init__.py.
Thanks,
Ilya
-Original Message-
From: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Chorny, Ilya
Sent: Friday, October 21, 2011 8:40 AM
To: Greg Von
Ilya,
Tools are not tightly coupled to the Galaxy web framework ( they can be
executed on the command line outside of Galaxy ) so, as you've commented, you
don't have access to the web framework from there. It's unclear to me what you
are trying to do. Can you clarify a bit more?
Greg Von
Excerpts from Chorny, Ilya's message of 2011-10-21 01:51:03 +:
I get the following error from routes
AttributeError: 'thread._local' object has no attribute 'mapper'
Okay, what I suspected. This is a product of the fact that job running
is decoupled from the web frontend. The job runner
Excerpts from Chorny, Ilya's message of 2011-10-21 15:43:35 +:
Also, I do not have access to trans in the Tools class in
lib/galaxy/tools/__init__.py.
'trans' is the state of a web transaction (a single request response
cycle). It is this only accessible for code that occurs within that
Greg,
I put the gmap tool suite in the galaxy Tool Shed, let me know if there is
more I should do.
It has 5 galaxy tools:
GMAP - Genomic Mapping and Alignment Program for mRNA and EST
sequences
GSNAP- Genomic Short-read Nucleotide Alignment Program
GMAP Build
Excerpts from Jim Johnson's message of 2011-10-21 17:13:02 +:
I put the gmap tool suite in the galaxy Tool Shed, let me know if there is
more I should do.
Awesome!
I added a requirement tag for the datatypes to the tool-configs:
% grep 'requirement.*datatype' *.xml
Thanks Jim,
This is on my development plan, but it may take a few days for me to get
heavily into it. I'll get back to you hopefully some time next week.
Greg
On Oct 21, 2011, at 1:13 PM, Jim Johnson wrote:
Greg,
I put the gmap tool suite in the galaxy Tool Shed, let me know if there is
On 10/21/11 12:29 PM, James Taylor wrote:
Excerpts from Jim Johnson's message of 2011-10-21 17:13:02 +:
I put the gmap tool suite in the galaxy Tool Shed, let me know if there is
more I should do.
Awesome!
I added a requirement tag for the datatypes to the tool-configs:
% grep
Chorny, Ilya wrote:
Nate,
I have been trying to figure out how to make the changes you suggested (i.e.
write output files to the job_working_directory) and then move them over to
files but I am having a difficult time navigating the code. If you could
point me in the right direction,
Can you guys show me an example of how this is used in the xml file?
Thanks,
Ilya
From: Jeremy Goecks [mailto:jeremy.goe...@emory.edu]
Sent: Thursday, October 20, 2011 7:03 PM
To: Chorny, Ilya
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: update of cufflinks and tophat to use dbkey attribute
Sorry, the link was wrong.
https://bitbucket.org/ichorny/galaxy-central-ilya2/
-Original Message-
From: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Chorny, Ilya
Sent: Friday, October 21, 2011 2:07 PM
To: Nate Coraor (n...@bx.psu.edu)
Cc:
One more thing there are some changes in lib/galaxy/tools/__init__.py and
lib/galaxy/model/__init__.py that are not related to actual user. They look
like they are toolshed related and may have been changed because to version of
the file that I copied over was older then galaxy-central.
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