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/rosema1/Projects/galaxy-dist/eggs/MarkupSafe-0.12-py2.7-linux-x86_64-ucs4.egg is being added to sys.path
self.check_version_conflict()
Stdout in the info link says:
Creating column 4 with expression c3-c2+1
Kept 100.00% of 96 lines.
Thanks
Mark
From: Jeremy Goecks [mailto:jeremy.goecks@emory.edu]
Sent: Monday, January 14, 2013 2:56 PM
To: Rose Mark USRE
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] text manipulation Compute tool error
If you click on the bug icon for the failed dataset (click on the dataset name to open the dataset and find the icon), what is the error listed? If you click on the information icon, is there any additional output in the standard output or error?
J.
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 other tools). When I run it on my local galaxy a file is produced that has the computed field last ( which is accurately computed but it appears that the white space between it and the other columns appears to be possibly only a space and not a tab), no error is reported but the job listing in the history is red, and the output is not available for input into other tools. I’ve tried this on other tab-delimited files and it does the same thing.
Can you reproduce this behavior on our public server? If so, it'll be much easier for us to take a look at the issue.
If you can't reproduce on our public server, then providing as many details as possible about the problem will provide the best chance for the list to help you. For instance:
*what is the exact error that the tool is returning?
*does it happen with all datasets or a particular dataset?
*does it happen with all dataset types (e.g., interval, bed, gtf) or just some?
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.
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 around the concatenation problem by using the Add Column tool but subsequent use of Compute also errors and its results are unavailable for further analysis though the output appears correct.
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 you is prohibited.
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 you is prohibited.___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
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 you is prohibited.