'error loading field data' when using tools in workflow interface

Question: 'error loading field data' when using tools in workflow interface

3.1 years ago by

Guy Reeves • 1.0k

Germany

Guy Reeves • 1.0k wrote:

I am trying to set up a galaxy instance at our institute, our IT person made a 'standard installation'. All appears to work including the basic tools ( I have checked out some of the tools e.g. upload, text manipulation- and they do indeed work) . However if try to use any tool to construct a workflow I get 'error loading field data' in red text in the workflow interface just below the tool name.

Does anybody know what has gone wrong and how I can fix it?

Thanks

Guy

error instalation workflow tools • 883 views

ADD COMMENT • link •

modified 3.1 years ago • written 3.1 years ago by Guy Reeves • 1.0k

3.1 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello Guy,

Does the tool panel include only tools that were installed from the Tool Shed or some that are custom (locally wrapped)? This error has been reported to before when custom tools are present and there was a problem with the tool name/id.

I am getting feedback from our team to help with specifics, but the more details you can share the better.

Thanks! Jen, Galaxy team

ADD COMMENT • link written 3.1 years ago by Jennifer Hillman Jackson ♦ 25k

Hi Jen

No other tools have been installed other than those that came with the basic installation (under the headings 'Get Data' .. to 'Graph/Display Data'.

Thanks

guy

ADD REPLY • link written 3.1 years ago by Guy Reeves • 1.0k

Odd. Is the most current version running? Use "git log" to check if current: https://wiki.galaxyproject.org/Admin/GetGalaxy#Keep_your_code_up_to_date

I'd like to see if I can replicate, but need to know where you are. Also, updating (if there are new updates, these often include bug fixes when mid-releases) is a good idea in general, as you know :) Workflows have undergone recent changes.

Update: meanwhile, I test the editor on the default install that is most current now, with no additional changes as a base-line.

Tx!

ADD REPLY • link modified 3.1 years ago • written 3.1 years ago by Jennifer Hillman Jackson ♦ 25k

Hi Guy, update from Dannon - would you be able to post "The galaxy-side log corresponding to that request". This would help us to understand more. None of us have seen this before. Thanks! Jen

ps: If this log is very long or you are not sure where this portion it is, send it into galaxy-bugs@lists.galaxyproject.org.

ADD REPLY • link written 3.1 years ago by Jennifer Hillman Jackson ♦ 25k

3.1 years ago by

Guy Reeves • 1.0k

Germany

Guy Reeves • 1.0k wrote:

Hi Jen and Dannon

I checked the most recent version was not running so I did

% git pull

and restarted galaxy

This all went fine until I

Error: pg_config executable not found.

Please add the directory containing pg_config to the PATH

or specify the full executable path with the option:

python setup.py build_ext --pg-config /path/to/pg_config build ...

or with the pg_config option in 'setup.cfg'.

----------------------------------------

Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-build-iTy4n9/psycopg2

I do not have the privileges to resolve this issue which relates to having PostgreSQL installed ( as I understand it)??

So I guess I will have to wait until the our IT guy (who did the installation) comes back from holiday next week and deals with this.

Currently I cannot get Galaxy up and running so I cannot send a log unfortunately.

I am very keen to get our galaxy server up and running and keep trying.

Thanks

Guy

ADD COMMENT • link written 3.1 years ago by Guy Reeves • 1.0k

Update :

The system admin has now installed PostgreSQL on the server .

But now gets the following error at start up which fails with

ImportError: /home/galaxy/galaxy/.venv/lib/python2.6/site-packages/pysam/libchtslib.so: undefined symbol: gzopen64

He suspects that samtools is a problem ('as it often has problems with zlib libraries'). But as has as I know there is no SAM tools in the basic installation (we have not installed any tools yet). Is that case ?

Thanks

Guy

ADD REPLY • link written 3.1 years ago by Guy Reeves • 1.0k

Yes, the first tool to install for Galaxy server is SAMTools. Obtain the most currently version from the Tool Shed. Jen

ADD REPLY • link written 3.1 years ago by Jennifer Hillman Jackson ♦ 25k

Thanks Jen. That is useful to know in trouble shooting this.

ADD REPLY • link written 3.1 years ago by Guy Reeves • 1.0k

Please log in to add an answer.

Similar posts • Search »