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