Hello
when attempting to create data libraries as admin I am not presented with the
same options listed in the documentation, namely
[cid:image001.png@01CF5DAE.5B451360]
Instead I only get Upload Files and Import datasets from your current
history. I want to use Upload files from filesystem
Nevermind, I found it in universe_wsgi.ini.
Mark
From: Rose Mark USRE
Sent: Monday, April 21, 2014 10:09 PM
To: galaxy-dev
Subject: uploading data libraries options
Hello
when attempting to create data libraries as admin I am not presented with the
same options listed in the documentation,
Hi All
I'm trying to format one of the three outputs of my galaxy tool as plain text.
Thus far no matter how I specify my output format in the tool xml file I have
the same problem. When I click the eye icon it opens a save dialog rather that
displaying the text output in the central frame.
Hi All
I'm trying to format one of the three outputs of my galaxy tool as plain text.
Thus far no matter how I specify my output format in the tool xml file I have
the same problem. When I click the eye icon it opens a save dialog rather that
displaying the text output in the central frame.
Hi Dannon
I'm presuming that wiping hidden files as you suggest would eliminate them
entirely so that there would be no history of them in the history, which
seems less than desirable if you want a record of how the analysis was
performed. It seems that it would be better if the steps in the
Hi All
Intermediate files in a workflow often make up the large majority of a
workflow's output and, when this is an NGS analysis, this volume can be HUGE.
This is a considerable concern for me as we consider implementing a local
install of galaxy. Storing all of this seems useless (once
Hey Dannon
Thanks, the web page I was finding earlier was mostly just an outline. This is
much better. At this point I'm just interested in learning what general
capabilities the API can provide. I'm sure after I read this and think more
about it I'll have questions. One thing I am thinking
Hi All
When is it anticipated that the documentation for the API will be available?
Thanks
Mark
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Ok, I added
track_jobs_in_database = True
to universe_wsgi.ini and now workflows appear to go to completion.
Another problem I was having was that steps in a workflow would stay gray even
though examination of the log revealed the steps had completed and produced
correct output (as verified by
Hi All
On my local install of galaxy I'm having problems executing workflows. I will
upload data into a new history and then select to run a saved workflow. This
initiates fine but, after the completion of a variable number of steps, the
workflow just stops after the successful completion
Having followed the directions in HostingALocalToolShed I ran
run_community.sh with the default configurations in community_wsgi.ini. It
executed without error but failed to start the tool shed as
http://127.0.0.1:9009 returns Unable to Connect error
Thanks for your help
Mark
This
Ah, yes. I forgot about the bug icon. Sorry, still pretty new to galaxy.
Here is the error message:
/home/rosema1/Projects/galaxy-dist/lib/galaxy/__init__.py:79: UserWarning:
Module markupsafe was already imported from
/usr/lib/python2.7/dist-packages/markupsafe/__init__.pyc, but
Yes, that did it.
Thanks a lot!
Mark
From: Jeremy Goecks [mailto:jeremy.goe...@emory.edu]
Sent: Monday, January 14, 2013 3:28 PM
To: Rose Mark USRE
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] text manipulation Compute tool error
The problem is that you have an egg conflict with
Hello
On a local install of galaxy I am getting seemingly erroneous behavior from the
text manipulation tool Compute. It will compute the expression I set
(c3-c2+1) but will concatenate it to the last column rather that create a new
column. Also the job errors and is shown in red. I can get
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