I'm glad you took the initiative to do this. It's one of the most requested 
features from local users here.
I'll happily test this in our environment.

Also - thanks for the github link - it's vastly superior to hg i think for the 
situation of merging pull requests. 
I can't figure a nice way to do a simple pull request in hg without a full 
scale repo duplication.

Best wishes!


On Dec 3, 2012, at 1:26 PM, John Chilton <>

> Hey Alex,
> Until I have bullied this stuff into galaxy-central, you should
> probably e-mail me directly and not the dev list. That said thanks for
> the heads up, that there was a definitely a bug. I pushed out this
> changeset to the bitbucket repository:
> I should mention that I have sort of abandoned the bitbucket
> repository for this work in lieu of github, so that I can rebase as
> Galaxy changes and keep clean changesets.
> Since I am posting this on the mailing list I might as well post a
> little summary of what has been done:
> - For each datatype, an implicit multiple file version of that
> datatype is created. A new multiple upload tool/ftp directory tool has
> been implemented to create these.
> - For any simple tool input you can chose a multiple file version of
> that input instead and then all outputs will become multiple file
> versions of the outputs. Uses task splitting stuff to distribute jobs
> across files.
> - For multiple input tools, you can choose either multiple inputs
> individuals (no change there) or a single composite version.
> Consistent interface for file path, display name, extension, etc... in
> tool wrapper.
> - It should work with most existing tools and datatypes without change.
> - Everything enabled with a single option in universe.ini
> Upshots:
>  - Makes workflows with arbitrary merging (and to a lesser extent
> branching) and arbitrary number of input files possible.
>  - Original base name is saved throughout analysis (when possible),
> so sample/replicate/fraction/lane/etc tracking is easier.
> I started working on the metadata piece last night, once that is done
> I was planning on making a little demo video to post to this list to
> try to sell the 3 outstanding small pull requests related to this work
> and the massive one that would follow those up :).
> -John
> On Sun, Dec 2, 2012 at 8:52 PM,  <> wrote:
>> Hi John,
>> My colleague (Neil) has a bit of a problem with the multi file support:
>> When I try and use the option "Upload Directory of files" I get the error 
>> below
>> Error Traceback:
>> View as:   Interactive  |  Text  |  XML (full)
>> ⇝ AttributeError: 'Bunch' object has no attribute 'multifiles'
>> URL:
>> Module weberror.evalexception.middleware:364 in respond         view
>>>> app_iter = self.application(environ, detect_start_response)
>> Module paste.debug.prints:98 in __call__         view
>>>> environ,
>> Module paste.wsgilib:539 in intercept_output         view
>>>> app_iter = application(environ, replacement_start_response)
>> Module paste.recursive:80 in __call__         view
>>>> return self.application(environ, start_response)
>> Module paste.httpexceptions:632 in __call__         view
>>>> return self.application(environ, start_response)
>> Module galaxy.web.framework.base:160 in __call__         view
>>>> body = method( trans, **kwargs )
>> Module galaxy.web.controllers.library_common:855 in upload_library_dataset   
>>       view
>>>> **kwd )
>> Module galaxy.web.controllers.library_common:1055 in upload_dataset         
>> view
>>>> json_file_path = upload_common.create_paramfile( trans, uploaded_datasets )
>> Module in create_paramfile         
>> view
>>>> multifiles = uploaded_dataset.multifiles,
>> AttributeError: 'Bunch' object has no attribute 'multifiles'
>> Any ideas? Should we check if 'multifiles' attribute is set? Or some other 
>> call is missing which should set it to NULL if it's missing?
>> -Alex
>> -----Original Message-----
>> From: [] On Behalf Of John 
>> Chilton
>> Sent: Wednesday, 17 October 2012 3:21 AM
>> To: Khassapov, Alex (CSIRO IM&T, Clayton)
>> Subject: Re: [galaxy-dev] pass more information on a dataset merge
>> Wow, thanks for the rapid feedback! I have made the changes you have 
>> suggested. It seems you must be interested in this idea/implementation. Let 
>> me know if you have specific use cases/requirements in mind and/or if you 
>> would be interested in write access to the repository.
>> -John
>> On Mon, Oct 15, 2012 at 11:51 PM,  <> wrote:
>>> Hi John,
>>> I tried your galaxy-central-homogeneous-composite-datatypes implementation, 
>>> works great thank you (and Jorrit).
>>> A couple of fixes:
>>> 1. Add multi_upload.xml to too_conf.xml 2.
>>> lib/galaxy/tools/parameters/ line 322 (in get_filenames( context 
>>> )) -
>>>        "if ftp_files is not None:"
>>>   Remove "is not None" as ftp_files is empty [], but not None, then line 
>>> 331 "user_ftp_dir = os.path.join(, 
>>> )" throws an exeption if ftp_upload_dir isn't set.
>>> Alex
>>> -----Original Message-----
>>> From:
>>> [] On Behalf Of John Chilton
>>> Sent: Tuesday, 16 October 2012 1:07 AM
>>> To: Jorrit Boekel
>>> Cc:
>>> Subject: Re: [galaxy-dev] pass more information on a dataset merge
>>> Here is an implementation of the implicit multi-file composite datatypes 
>>> piece of that idea. I think the implicit parallelism may be harder.
>>> atypes/compare
>>> Jorrit do you have any objection to me trying to get this included in 
>>> galaxy-central (this is 95% code I stole from you)? I made the changes 
>>> against a clean galaxy-central fork and included nothing proteomics 
>>> specific in anticipation of trying to do that. I have talked with Jim 
>>> Johnson about the idea and he believes it would be useful his mothur 
>>> metagenomics tools, so the idea is valuable outside of proteomics.
>>> Galaxy team, would you be okay with including this and if so is there 
>>> anything you would like to see either at a high level or at the level of 
>>> the actual implementation.
>>> -John
>>> ------------------------------------------------
>>> John Chilton
>>> Senior Software Developer
>>> University of Minnesota Supercomputing Institute
>>> Office: 612-625-0917
>>> Cell: 612-226-9223
>>> Bitbucket:
>>> Github:
>>> Web:
>>> On Mon, Oct 8, 2012 at 9:24 AM, John Chilton <> wrote:
>>>> Jim Johnson and I have been discussing that approach to handling
>>>> fractionated proteomics samples as well (composite datatypes, not the
>>>> specifics of the interface for parallelizing).
>>>> My perspective has been that Galaxy should be augmented with better
>>>> native mechanisms for grouping objects in histories, operating over
>>>> those groups, building workflows that involve arbitrary numbers of
>>>> inputs, etc... Composite data types are kindof a kludge, I think they
>>>> are more useful for grouping HTML files together when you don't care
>>>> about operating on the constituent parts you just want to view pages
>>>> a as a report or something. With this proteomic data we are working
>>>> with, the individual pieces are really interesting right? You want to
>>>> operate on the individual pieces with the full array of tools (not
>>>> just these special tools that have the logic for dealing with the
>>>> composite datatypes), you want to visualize the files, etc... Putting
>>>> these component pieces in the composite data type extra_files path
>>>> really limits what you can do with the pieces in Galaxy.
>>>> I have a vague idea of something that I think could bridge some of
>>>> the gaps between the approaches (though I have no clue on the
>>>> feasibility). Looking through your implementation on bitbucket it
>>>> looks like you are defining your core datatypes (MS2, CruxSequest) as
>>>> subclasses of this composite data type (CompositeMultifile). My
>>>> recommendation would be to try to define plain datatypes for these
>>>> core datatype (MS2, CruxSequest) and then have the separate composite
>>>> datatype sort of delegate to the plain datatypes.
>>>> You could then continue to explicitly declare subclasses of the
>>>> composite datatype (maybe MS2Set, CruxSequestSet), but also maybe
>>>> augement the tool xml so you can do implicit data type instances the
>>>> way you can with tabular data for instance (instead of defining
>>>> columns you would define the datatype to delegate to).
>>>> The next step would be to make the parallelism implicit (i.e pull it
>>>> out of the tool wrapper). Your tool wrappers wouldn't reference the
>>>> composite datatypes, they would reference the simple datatypes, but
>>>> you could add a little icon next to any input that let you replace a
>>>> single input with a composite input for that type. It would be kind
>>>> of like the run workflow page where you can replace an input with a
>>>> multiple inputs. If a composite input (or inputs) are selected the
>>>> tool would then produce composite outputs.
>>>> For the steps that actually combine multiple inputs, I think in your
>>>> case this is perculator maybe (a tool like interprophet or Scaffold
>>>> that merges peptide probabilities across runs and groups proteins),
>>>> then you could have the same sort of implicit replacement but instead
>>>> of for single inputs it could do that for multi-inputs (assuming the
>>>> Galaxy powers that be accept my fixes for multi-input tool parameters:
>>>> The upshot of all of that would be that then even if these composites
>>>> datatypes aren't used widely, other people could still use your
>>>> proteomics tools (my users are definitely interested in Crux for
>>>> instance) and you could then use other developers' proteomic tools
>>>> with your composite datatypes even though they weren't designed with
>>>> that use case in mind (I have msconvert, myrimatch, idpicker,
>>>> proteinpilot, Ira Cooke has X! Tandem, OMSSA, TPP, and NBIC has an
>>>> entire suite of label free quant tools). A third benefit would be
>>>> that people working in other -omicses could make use of the
>>>> homogenous composite datatype implementation without needing to
>>>> rewrite their wrappers and datatypes.
>>>> There is probably something that I am missing that makes this very
>>>> difficult, let me know if you think this is a good idea and what its
>>>> feasibility might be. I forked your repo and set off to try to
>>>> implement some of this stuff last week and I ended up with my galaxy
>>>> pull requests to improve batching workflows and multi-input tool
>>>> parameters instead, but I hope to eventually get around to it.
>>>> -John
>>>> ------------------------------------------------
>>>> John Chilton
>>>> Senior Software Developer
>>>> University of Minnesota Supercomputing Institute
>>>> Office: 612-625-0917
>>>> Cell: 612-226-9223
>>>> Bitbucket:
>>>> Github:
>>>> Web:
>>>> On Mon, Oct 1, 2012 at 8:24 AM, Jorrit Boekel
>>>> <> wrote:
>>>>> Dear list,
>>>>> I thought I was working with fairly large datasets, but they have
>>>>> recently started to include ~2Gb files in sets of >50. I have ran
>>>>> these sort of things before as merged data by using tar to roll them
>>>>> up in one set, but when dealing with >100Gb tarfiles, Galaxy on EC2
>>>>> seems to get very slow, although that's probably because of my
>>>>> implementation of dataset type detection (untar and read through files).
>>>>> Since tarring/untarring isn't very clean, I want to switch from
>>>>> tarring to creating composite files on merge by putting a tool's
>>>>> results into the dataset.extra_files_path. This doesn't seem to be
>>>>> supported yet, because we currently pass in do_merge the output
>>>>> dataset.filename to the respective datatype's merge method.
>>>>> I would like to pass more data to the merge method (let's say the
>>>>> whole dataset object) to be able to get the composite files directory and 
>>>>> 'merge'
>>>>> the files in there. Good idea, bad idea? If anyone has views on
>>>>> this, I'd love to hear them.
>>>>> cheers,
>>>>> jorrit
>>>>> ___________________________________________________________
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