Jim,

Sounds great - this will be very helpful!

Greg

On Oct 18, 2011, at 11:03 AM, Jim Johnson wrote:

> Greg,
> 
> The mothur_toolsuite in the ToolShed  contains a file with added datatypes 
> for metagenomics (used by mothur and some by qiime):
> mothur_toolsuite/mothur/lib/galaxy/datatypes/metagenomics.py
> The README has info on how I incorporated mothur into our local galaxy server.
> 
> I'm also working on GMAP/GSNAP  (  http://research-pub.gene.com/gmap/ )
> So far I've created a GmapDB class,  analogous to the ngsindex.BowtieIndex 
> class, but with more metadata.
> I'm also adding a IntervalIndexTree class for indexing maps of splice 
> junctions, introns, and SNPs.
> I'll send you this as soon as I've got it working.
> 
> Thanks,
> 
> JJ
> 
> 
> On 10/17/11 1:06 PM, Greg Von Kuster wrote:
>> We've digested this topic a bit here at Galaxy Central, and agree that at 
>> some point ( maybe soon for very basic functionality ) we need to provide 
>> support for new data types in tool shed repositories.  It would be very 
>> helpful ( and significantly speed up the development process ) if the 
>> community could provide at least 2 different tools that use data types not 
>> included in the Galaxy distribution ( sending me a tarball that includes all 
>> the tool dependencies, including the new data type class would be ideal ).  
>> When I get them I'll add this new feature set to my development list.
>> 
>> Thanks everyone for all the input on this!
>> 
>> Greg Von Kuster
>> 
>> 
>> On Oct 7, 2011, at 2:05 PM, Jim Johnson wrote:
>> 
>>> Greg,
>>> 
>>> It would be great if there were a way to expand upon the core datatypes 
>>> using the ToolShed.
>>> 
>>> Would it be possible to have a separate datatype repository within the 
>>> ToolShed?
>>> 
>>> Datatype
>>>  name=""
>>>  description=""
>>>  datatype_dependencies=[]
>>>  definition=<python code>
>>> 
>>> The tool config could be expanded to have requirement for datatypes.
>>>   <requirement type="datatype">ssmap</requirement>
>>> 
>>> 
>>> 
>>> 
>>> Table datatype
>>>   Column    |            Type             |                     Modifiers
>>> -------------+-----------------------------+---------------------------------------------------
>>> id          | integer                     | not null default 
>>> nextval('datatype_id_seq'::regclass)
>>> name        | character varying(255)      |
>>> version     | character varying(40)       |
>>> description | text                        |
>>> definition  | text                        |
>>> UNIQUE (name)
>>> 
>>> Table datatype_datatype_association
>>>   Column    |            Type             |                     Modifiers
>>> -------------+-----------------------------+---------------------------------------------------
>>> id          | integer                     | not null default 
>>> nextval('datatype_id_seq'::regclass)
>>> datatype_id | integer                     |
>>> requires_id | integer                     |
>>> FOREIGN KEY (datatype_id) REFERENCES datatype(id)
>>> FOREIGN KEY (requires_id) REFERENCES datatype(id)
>>> 
>>> 
>>> Then for my mothur metagenomics tools I could define:
>>> 
>>> name="ssmap"   description="Secondary Structure Map"  version="1.0"  
>>> datatype_dependencies=[tabular]
>>> definition=
>>> from galaxy.datatypes.tabular import Tabular
>>> class SecondaryStructureMap(Tabular):
>>>    file_ext = 'ssmap'
>>>    def __init__(self, **kwd):
>>>        """Initialize secondary structure map datatype"""
>>>        Tabular.__init__( self, **kwd )
>>>        self.column_names = ['Map']
>>> 
>>>    def sniff( self, filename ):
>>>        """
>>>        Determines whether the file is a secondary structure map format
>>>        A single column with an integer value which indicates the row that 
>>> this row maps to.
>>>        check you make sure is structMap[10] = 380 then structMap[380] = 10.
>>>        """
>>> ...
>>> 
>>> 
>>> 
>>> 
>>> Then the align.check.xml tool_config could require the 'ssmap' datatype:
>>> 
>>> <tool id="mothur_align_check" name="Align.check" version="1.19.0">
>>> <description>Calculate the number of potentially misaligned 
>>> bases</description>
>>> <requirements>
>>>   <requirement type="binary">mothur</requirement>
>>>   <requirement type="datatype">ssmap</requirement>
>>>  </requirements>
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>>> John,
>>>> 
>>>> I've been following this message thread, and it seems it's gone in a 
>>>> direction that differs from your initial question about the possibility 
>>>> for Galaxy to handle automatic editing of the datatypes_conf.xml file when 
>>>> certain Galaxy tool shed tools are automatically installed.  There are 
>>>> some complexities to consider in attempting this.  One of the issues to 
>>>> consider is that the work for adding support for a new datatype to Galaxy 
>>>> lies outside of the intended function of the tool shed.  If new support is 
>>>> added to the Galaxy code base, an entry for that new datatype should be 
>>>> manually added to the table at the same time.  There may be benefits to 
>>>> enabling automatic changes to datatype entries that already exist in the 
>>>> file (e.g., adding a new converter for an existing datatype entry), but 
>>>> perhaps adding a completely new datatype to the file may not be 
>>>> appropriate.  I'll continue to think about this - send additional thought 
>>>> and feedback, as doing so is always helpful
>>>> 
>>>> Thanks!
>>>> 
>>>> Greg
>>>> 
>>>> 
>>>> On Oct 5, 2011, at 11:48 PM, Duddy, John wrote:
>>>> 
>>>>> One of the things we’re facing is the sheer size of a whole human genome 
>>>>> at 30x coverage. An effective way to deal with that is by compressing the 
>>>>> FASTQ files. That works for BWA and our ELAND, which can directly read a 
>>>>> compressed FASTQ, but other tools crash when reading compressed FASTQ 
>>>>> filesfiles. One way to address that would be to introduce a new type, for 
>>>>> example “CompressedFastQ”, with a conversion to FASTQ defined. BWA could 
>>>>> take both types as input. This would allow the best of both worlds – 
>>>>> efficient storage and use by all existing tools.
>>>>> 
>>>>> Another example would be adding the CASAVA tools to Galaxy. Some of the 
>>>>> statistics generation tools use custom file formats. To be able to make 
>>>>> the use of those tools optional and configurable, they should be separate 
>>>>> from the aligner, but that would require that Galaxy be made aware of the 
>>>>> custom file formats – we’d have to add a datatype.
>>>>> 
>>>>> John Duddy
>>>>> Sr. Staff Software Engineer
>>>>> Illumina, Inc.
>>>>> 9885 Towne Centre Drive
>>>>> San Diego, CA 92121
>>>>> Tel: 858-736-3584
>>>>> E-mail: jduddy at illumina.com
>>>>> 
>>>>> From: Greg Von Kuster [mailto:greg at bx.psu.edu]
>>>>> Sent: Wednesday, October 05, 2011 6:25 PM
>>>>> To: Duddy, John
>>>>> Cc: galaxy-dev at lists.bx.psu.edu
>>>>> Subject: Re: [galaxy-dev] Tool shed and datatypes
>>>>> 
>>>>> Hello John,
>>>>> 
>>>>> The Galaxy tool shed currently is not enabled to automatically edit the 
>>>>> datatypes_conf.xml file, although I could add this feature if the need 
>>>>> exists.  Can you elaborate on what you are looking to do regarding this?
>>>>> 
>>>>> Thanks!
>>>>> 
>>>>> 
>>>>> On Oct 5, 2011, at 1:52 PM, Duddy, John wrote:
>>>>> 
>>>>> 
>>>>> Can we introduce new file types via tools in the tool shed? It seems 
>>>>> Galaxy can load them if they are in the datatypes configuration file. 
>>>>> Does tool installation automate the editing of that file?
>>>>> 
>>>>> 
>>>>> John Duddy
>>>>> Sr. Staff Software Engineer
>>>>> Illumina, Inc.
>>>>> 9885 Towne Centre Drive
>>>>> San Diego, CA 92121
>>>>> Tel: 858-736-3584
>>>>> E-mail: jduddy at illumina.com
>>>>> 
>>>>> ___________________________________________________________
>>>>> Please keep all replies on the list by using "reply all"
>>>>> in your mail client.  To manage your subscriptions to this
>>>>> and other Galaxy lists, please use the interface at:
>>>>> 
>>>>> http://lists.bx.psu.edu/
>>>>> 
>>>>> Greg Von Kuster
>>>>> Galaxy Development Team
>>>>> greg at bx.psu.edu
>>>>> 
>>> ___________________________________________________________
>>> Please keep all replies on the list by using "reply all"
>>> in your mail client.  To manage your subscriptions to this
>>> and other Galaxy lists, please use the interface at:
>>> 
>>> http://lists.bx.psu.edu/
>>> 
>> Greg Von Kuster
>> Galaxy Development Team
>> g...@bx.psu.edu
>> 
>> 
>> 
> 
> 
> 
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
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> and other Galaxy lists, please use the interface at:
> 
> http://lists.bx.psu.edu/
> 

Greg Von Kuster
Galaxy Development Team
g...@bx.psu.edu




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