[galaxy-dev] 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, 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 filesys

[galaxy-dev] FW: uploading data libraries options

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, na

[galaxy-dev] gatk lite

Hello Is it possible to redirect the GATK tools in my local installation of Galaxy to use GATK Lite (which is free) rather than GATK. If so what files would need to be altered and how? I'm particularly interested in getting the "Depth of Coverage" tool to work. Thanks much Mark This mes

[galaxy-dev] text manipulation Compute tool error

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

Re: [galaxy-dev] text manipulation Compute tool error

I've received no replies to this post though clearly I must be doing something wrong since the tool would be useless if this were its normal behavior and judging from other posts people are using it. Please help. Thanks Mark From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun..

Re: [galaxy-dev] text manipulation Compute tool error

No. When I save the file I wish to manipulate from my local galaxy and upload it to the public galaxy and run "Compute" it works (i.e. a tab-delimited file is produced with the computed field occurring last, the job listing in the history is green, and the result is available for input into oth

Re: [galaxy-dev] text manipulation Compute tool error

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 /home/rosem

Re: [galaxy-dev] text manipulation Compute tool error

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 an

[galaxy-dev] local galaxy tool shed install

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 m

[galaxy-dev] workflows stop prematurely

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 of

Re: [galaxy-dev] workflows stop prematurely

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

[galaxy-dev] iterating over files

Hello I've seen posts from a couple of years ago asking about galaxy's ability to iterate over multiple files. The reply was that the developers were working on it. Have they succeeded and if so how can it now be done. Thanks Mark This message may contain confidential information. If you

[galaxy-dev] galaxy api documentation

Hi All When is it anticipated that the documentation for the API will be available? Thanks Mark This message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by

Re: [galaxy-dev] galaxy api documentation

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

[galaxy-dev] workflow intermediate files hog memory

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 wor

Re: [galaxy-dev] workflow intermediate files hog memory

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

[galaxy-dev] plain text output format

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.

[galaxy-dev] unable to display text output

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.