Hi Björn,

On Apr 22, 2015, at 8:00 AM, Björn Grüning <bjoern.gruen...@gmail.com> wrote:

>> Do you have a beer preference?  
> 
> Outing: I'm one of the rare Germans that do not drink alcohol ;)

That must be awkward ;)


> This can be done via the ToolShed. I assume your custom command
> interpreter is not different than python or perl as interpreter? 

One difference is that my interpreter is a Java program. I likely should have 
mentioned that little detail... anyone wanting to install our tools would need 
my interpreter AND Java 1.7+ on their server.  Hopefully that is not an 
insurmountable problem. 

However, does the bioinformatics community really want a bunch of NLP tools in 
their tool shed?


>> The editor also allows me to select output formats that have no converters 
>> defined, 
>> so either I am still missing something or the workflow editor does not do 
>> what I want.  I can convert formats through the "Edit attributes" menu, 
>> so Galaxy knows about my converters and how to invoke them, just not in the 
>> workflow editor.
> 
> Ok, I think I understood. Not sure if this is the best way but put your
> converters into the toolbox.

By the "toolbox" do you mean adding my converters to the tool_conf.xml file so 
they are available on the Tools menu?  I have done that and I can add the 
converters to a workflow manually. I was just hoping the workflow editor could 
detect when it could perform the conversion and insert the converters as 
needed; it seems this is not possible.


>> Do you have more pointers to tools that use the attached metadata?  In 
>> particular tools that set metadata that is consumed by subsequent tools.
> 
> The sqlite datatype should be a good example. Keep in mind, we can not
> set metadata from inside a tool.
> Imho this is not possible, yet, but a
> common requested feature. But you can "calculate" such metadata inside
> your datatype definition and set it implicitly after your tool is finished.

Setting the metadata in the tool wrapper is fine, and after grepping through 
some of the other wrappers I think I need something like:

  <!-- Output from a tokenizer -->
  <outputs>
    <data name="output" format="xml" label="Output">
        <actions>
            <action type="metadata" name="tokens">True</action>
        </actions>
    </data>
  </outputs>

  <!-- Input to a part of speech tagger -->
  <inputs>
    <param name="input" type="data" format="xml">
        <validator type="expression" message="Please run a tokenizer 
first.">metadata.tokens is not None</validator>
    </param>
  </inputs>

That is, the input validator simply checks if some value has been set in the 
metadata, and the output sets a value in the metadata.  The above does not 
work, but at least Galaxy stopped complaining about the tool XML with this.  
However, the documentation for <option/> <filter/> and <action/> does not match 
up with what existing wrappers (in the dev branch) are doing so I am having 
problems with the exact syntax.


>> Do you have pointers to any documentation on data collections?  My searches 
>> haven't turned up much but tantalizing references [1], 
>> and my experiments trying to return a data collection from a tool have been 
>> unsuccessful.
> 
> https://wiki.galaxyproject.org/Histories?highlight=%28collection%29#Dataset_Collections
> 
> https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax ->
> data_collection
> 
> And have a look at:
> https://github.com/galaxyproject/galaxy/tree/dev/test/functional/tools

Success!  I was running the code from master, so I suspect that was part of my 
problem.  

However, my browser is still complaining about long running scripts.

> A script on this page may be busy, or it may have stopped responding. You can 
> stop the script now, open the script in the debugger, or let the script 
> continue.
> 
> Script: http://localhost:8000/static/s…/jquery/jquery.js?v=1429811186:2


I accidentally left visible="true" when creating the dataset collection and 
ended up with +1500 items in my history; the above message kept popping up 
while the workflow was running (at least until I selected "Don't show this 
again").  Deleting +1500 datasets from the history is also very slow, but that 
is a different issue. On the bright side, at least I had +1500 items in the 
history to delete.


>> I have also been trying John Chiltons blend4j and managed to populate a data 
>> library, and this is almost what I want, 
>> but I would like a tool that can be included in a workflow as the data from 
>> the library may not necessarily be the first step.   
>> I have no problem calling the Galaxy API from my tools, except that between 
>> the bioinformatics lingo and Python (I'm a Java programmer) it's slow going.
> 
> If possible at all you should avoid this, but as last resort probably an
> option.

Out of curiosity, what exactly should I avoid; making calls to the Galaxy 
REST/API from inside a tool, using blend4j, or populating a data library from 
inside a tool?  I can see myself doing all three in the near future.

Cheers,
Keith

> 
> Ciao,
> Bjoern
> 
>> Cheers,
>> Keith
>> 
>> REFERENCES
>> 
>> 1. https://wiki.galaxyproject.org/Learn/API#Collections
>> 2. 
>> https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files#Number_of_Output_datasets_cannot_be_determined_until_tool_run
>> 
>>> 
>>>>> Oh yes this is supported out of the box!
>>>>> See here for a small documentation:
>>>>> https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox#supported-filetypes
>>>>> 
>>>>> Here is a example of how you can write your own datatypes:
>>>>> 
>>>>> https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/datatypes
>>>> 
>>>> I feel like I must be missing the obvious.  Here is the relevant section 
>>>> of my datatypes_conf.xml (you can see the full file at 
>>>> https://github.com/oanc/Galaxy/blob/master/config/datatypes_conf.xml)
>>>> 
>>>> <datatype extension="lif" type="galaxy.datatypes.text:Json" 
>>>> display_in_upload="True">
>>>>    <converter file="convert.json2gate_2.0.0.xml" target_datatype="gate"/>
>>>> </datatype>
>>>> <datatype extension="gate" type="galaxy.datatypes.xml:GenericXml" 
>>>> mimetype="application/xml" display_in_upload="true">
>>>>    <converter file="convert.gate2json_2.0.0.xml" target_datatype="lif"/>
>>>> </datatype>
>>>> 
>>>> Is there anything I need to do beyond defining the datatypes for implicit 
>>>> conversions to take place?
>>> 
>>> I guess you need to place your converters under
>>> https://github.com/oanc/Galaxy/tree/master/lib/galaxy/datatypes/converters/
>>> 
>>> And get rid of 'convert.' in your datatypes_conf.xml at least if you are
>>> not using the TS.
>>> 
>>> Hope this helps you a little bit more,
>>> Bjoern
>>> 
>>>> Thanks,
>>>> Keith Suderman
>>>> 
>>>>> 
>>>>>> 
>>>>>> 4. OAuth 2.0 / OpenID Connect: 
>>>>>> 
>>>>>> I need to be able to fetch documents from data providers that require an 
>>>>>> OAuth 2.0 access token. Currently, I use a separate service to go 
>>>>>> through the OAuth authentication/authorization process and then have the 
>>>>>> user copy/paste their access token into a text field in Galaxy.   
>>>>>> Is there a way to perform the OAuth authentication dance required by the 
>>>>>> remote service inside Galaxy itself?   
>>>>> 
>>>>> I don't think so, but maybe someone else has an idea here.
>>>>> 
>>>>>> I’ve looked at the Trello site for Galaxy and see that both OAuth 2.0 
>>>>>> and OpenID Connect are on the radar, hopefully this use case is being 
>>>>>> considered as well.
>>>>>> 
>>>>>> I’m sure to have more questions after working through some visualization 
>>>>>> examples, but this should keep me busy for now.
>>>>> 
>>>>> Hope you are busy now :)
>>>>> Cheers and keep us up to date!
>>>>> Bjoern
>>>>> 
>>>>>> Sincerely,
>>>>>> Keith Suderman
>>>>>> 
>>>>>> REFERENCES
>>>>>> 
>>>>>> 1. https://wiki.galaxyproject.org/Admin/Tools/AddingTools
>>>>>> 
>>>>>> ------------------------------
>>>>>> Research Associate
>>>>>> Department of Computer Science
>>>>>> Vassar College
>>>>>> Poughkeepsie, NY
>>>>>> 
>>>>>> 
>>>>>> ___________________________________________________________
>>>>>> Please keep all replies on the list by using "reply all"
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>>>>>> 
>>>>> 
>>>> 
>>>> ------------------------------
>>>> Research Associate
>>>> Department of Computer Science
>>>> Vassar College
>>>> Poughkeepsie, NY
>>>> 
>>>> 
>>>> 
>>> 
>> 
>> ------------------------------
>> Research Associate
>> Department of Computer Science
>> Vassar College
>> Poughkeepsie, NY
>> 
>> 
> 

------------------------------
Research Associate
Department of Computer Science
Vassar College
Poughkeepsie, NY


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