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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