I cannot help with this new issue without more information from you. What
version of Galaxy are you running?
On Dec 5, 2012, at 5:44 AM, Adam Carr (NBI) wrote:
> Hi Greg,
> Thank you for your reply. I have checked on my
> tool_data_table_conf.xml.sample and tool_data_table_conf.xml files and they
> look to be correctly formatted with <tables> tags at their beginnings and
> However, I noticed that this file is already populated, should that be the
> case with a fresh newly installed Tool Shed?
Can you clarify what you mean here with your statement "this file is already
populated"? Are you referring to a file in the tool shed or a file in Galaxy?
> My issue doesn't occur when I'm importing a tool from the Tool Shed to
> Galaxy, but when I'm uploading a tool that I've downloaded from the Galaxy
> Tool Shed to my Tool Shed.
Are you still referring to the same repository from the main tool shed that is
discussed at the start of this thread below? How did you download the
repository from the Galaxy tool shed ( I assume you are talking about the main
Galaxy tool shed, but please confirm ). Did you download it as a tarball? Can
you clarify your statement "when I'm uploading a tool"? Do you mean that you
are attempting to upload the downloaded repository tarball, or something else?
> The last of the errors reported after I attempt an upload being:
> Module galaxy.util.shed_util:336 in check_tool_input_params
> >> if options.tool_data_table or options.missing_tool_data_table_name:
> AttributeError: 'str' object has no attribute 'tool_data_table'
I'll need all of the answers above along with the entire stack trace to be able
to help you here.
Greg Von Kuster
> Many Thanks,
> -----Original Message-----
> From: Greg Von Kuster [mailto:g...@bx.psu.edu]
> Sent: 04 December 2012 16:40
> To: Adam Carr (NBI)
> Cc: email@example.com
> Subject: Re: [galaxy-dev] Main toolshed broken??
> Hi Adam,
> I believe this is related to the invalid xml definition in your repository's
> tool_data_table_conf.xml.sample file which I discussed in a previous reply.
> Greg Von Kuster
> On Dec 4, 2012, at 8:08 AM, Adam Carr (NBI) wrote:
> > Hi,
> > I hadn't caught this as I posted my query to the list, I'm having trouble
> > uploading to a brand new repository. Could my issue described here:
> > http://dev.list.galaxyproject.org/Tool-Shed-Upload-Files-To-Repository-Crash-td4657324.html,
> > be related?
> > Many Thanks,
> > Adam.
> > ---
> > Adam Carr
> > Linux Support & Developmnent
> > E adam.c...@nbi.ac.uk
> > T +44 1603 450161
> > W jic.ac.uk ifr.ac.uk tgac.ac.uk tsl.ac.uk
> > NBI Partnership Ltd
> > Norwich Research Park
> > Norwich NR4 7UH
> > The NBI Partnership Ltd provides non-scientific services to the
> > Institute of Food Research, the John Innes Centre, The Genome Analysis
> > Centre and The Sainsbury Laboratory
> > -----Original Message-----
> >> Hi list,
> >> Trying to upload, delete, update files from a repository I own in the
> >> toolshed I keep getting Server Error..
> >> This is the repo:
> >> http://fcaramia@.../repos/fcaramia/methylation_analysis_bismark
> >> Is anyone having the same issues?? I could just delete the repository but
> >> no option for that is given..
> >> Thanks,
> >> Franco
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