Hi Carlos,

I've uploaded a fix for the problem you saw when attempting to reset all 
metadata on your cummerbund tool.  Thanks for reporting this issue.

Looking at your change sets, it seems that you are attempting to use the public 
tool shed hosted by Penn State as a source code repository for your tool 
development efforts.  If so, this is not the intent the public tool shed - it's 
intent is rather to share fully functional tools with others in the Galaxy 
community ("fully functional" implies that the tools was developed in an 
environment that included a Galaxy instance, and the tool proved to be 
functional within the Galaxy instance before it was uploaded to the tool shed).

The tool shed inspects every change set and performs certain functions based on 
the content of the change set.  For example, if a change set includes a tool, 
an attempt to load the tool will be made to generate information about the 
tool.  Data types included in a change set are processed as well.  Because of 
this, it is best to upload changes to the tool shed that contain development 
efforts that are in a "finished" state.

See my additional inline comments and questions in your message.

Thanks!

Greg Von Kuster

On Feb 15, 2012, at 2:24 PM, Carlos Borroto wrote:

> Hi Greg,
> 
> Thanks for your answer. Would be great to get the tool to preview
> correctly but is not a big deal.
> 
> I'm having a few more problems. I'm getting this error from time to
> time when I do "hg push" or even when I delete all files from the
> toolshed and upload new ones:
> "Version information for the tools included in the cummerbund
> repository is missing. Reset all of this repository's metadata in the
> tool shed, then set the installed tool versions from the installed
> repository's Repository Actions menu."


The fix that I've pushed to the tool shed should hopefully resolve this issue.


> 
> Doing a "Reset metadata" in the toolshed doesn't solve this issue. I
> can't find how to do "then set the installed tool versions from the
> installed repository's Repository Actions menu".
> 
> I'm also having problem including a datatype with the tool. One of the
> outputs of the tool is a sqlite database. I have this
> datatypes_conf.xml:
> <?xml version="1.0"?>
> <datatypes>
>  <registration>
>    <datatype extension="sqlite" type="galaxy.datatypes.binary:Binary"
> mimetype="application/octet-stream" subclass="True"
> display_in_upload="true"/>
>  </registration>
> </datatypes>
> 
> Still sqlite doesn't appear as an option when I try to upload a file
> to Galaxy. The new datatype does appear if I choose the edit a dataset
> attributes.
> 

I'm  not quite sure what your intentions are here, but attempting to make a 
Galaxy datatypes be a sqlite database sounds like it will be complex and 
fragile,


> Lastly, when I try to upload a sqlite database I get this error:
> "An error occurred running this job: The uploaded binary file contains
> inappropriate content"

Uploading a sqlite database to the tool shed will certainly result in this 
behavior as our code inspectors will not handle this types o content.

> 
> $ file -i cummerbund.sqlite
> cummerbund.sqlite: application/octet-stream; charset=binary
> 
> I was hoping by including a sqlite datatype this would be resolved.
> 
> Thanks,
> Carlos
> 
> On Tue, Feb 14, 2012 at 3:10 PM, Greg Von Kuster <g...@bx.psu.edu> wrote:
>> Hi Carlos,
>> 
>> Not every tool form parameter will properly display when previewing the tool 
>> in the tool shed because the tool shed doesn't have access to some Galaxy 
>> components (e.g., a Galaxy history ) that are required for some tool 
>> parameter types.  When I get a chance, I'll take a closer look, but if your 
>> tool is functional when installed from the tool shed to a local Galaxy 
>> instance, all should be ok.
>> 
>> Thanks for your contribution!
>> 
>> Greg Von Kuster
>> 
>> On Feb 14, 2012, at 1:49 PM, Carlos Borroto wrote:
>> 
>>> Hi,
>>> 
>>> I'm currently developing my first Galaxy tool. I'm working on a
>>> wrapper for R's library cummeRbund[1]. I got to the point where the
>>> tool although incomplete on functionality, I think is ready to be
>>> uploaded to the Toolshed. I was able to do so. I also made sure I
>>> could then install it on my local instance using the toolshed
>>> repository.
>>> 
>>> Everything is working as expected, except, the tool preview is not
>>> working correctly. There is no error, but the inputs, most of them
>>> conditional inputs, aren't being displayed correctly. This is the
>>> direct link to the tool in the test toolshed:
>>> http://testtoolshed.g2.bx.psu.edu/repository/manage_repository?operation=view_or_manage_repository&id=575665a9f01c6d41
>>> 
>>> [1]http://compbio.mit.edu/cummeRbund/
>>> 
>>> Kind regards,
>>> Carlos
>>> ___________________________________________________________
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>> 
> 
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