Hi Greg,

I did follow that link and I think the datatypes_conf.xml in the tool
repository is correctly written:
<?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>

I thought by adding display_in_upload="true" that would make the
datatype to appear as an option when uploading a file, but this is not
happening. Do I need to declare type as for example
"galaxy.datatypes.binary:Sqlite3" for this to work? If I have to, I'm
guessing I would have to do what is explained here:
http://wiki.g2.bx.psu.edu/Tool%20Shed#Including_proprietary_data_types_that_use_class_modules_contained_in_your_repository

Thanks,
Carlos

On Wed, Feb 29, 2012 at 12:14 PM, Greg Von Kuster <g...@bx.psu.edu> wrote:
> Hi Carlos,
>
> You can certainly add support for a sqlite database datatype to your local 
> galaxy instance.  As you say, it may be no more complex / fragile than h5 or 
> other binary datatypes - I've not gone far enough down the analysis path to 
> provide good reasons why it may or may not be reasonable, so perhaps I spoke 
> too soon.  If you have questions about how to add support for new datatypes, 
> see our wiki at http://wiki.g2.bx.psu.edu/Admin/Datatypes.
>
> Thanks!
>
> Greg Von Kuster
>
>
> On Feb 29, 2012, at 11:59 AM, Carlos Borroto wrote:
>
>> Hi Greg,
>>
>> Thanks for looking and resolving this issue. After deleting all the
>> files in the repo and re-adding them, everything is working as
>> expected.
>>
>> Please see my comments inline about the other two issues.
>>
>> On Tue, Feb 28, 2012 at 1:57 PM, Greg Von Kuster <g...@bx.psu.edu> wrote:
>>> 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,
>>>
>>
>> One of the steps for cummeRbund library is the creation of a sqlite
>> database. Generating this database is by far the step taking most of
>> the processing time. cummeRbund author made it possible to pass as an
>> input a previously generated sqlite database, this greatly cuts the
>> processing time for subsequent analysis of the same cuffdiff ouput. I
>> don't see why having a sqlite binary data type would be different than
>> let say BigBed, BAM or h5 binary data types. Could you please comment
>> on why you think it would 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.
>>>
>>
>> Sorry I didn't explained myself clearly, I'm not uploading the sqlite
>> database to the tool shed. I'm uploading it to a history so I can use
>> it with my newly developed tool.
>>
>> Kind regards,
>> Carlos
>>
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>

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