Hi John,

Do you think it's possible to create a <test> for your 'm:" format? I couldn't 
find how to specify multi input files for the test.

-Alex

-----Original Message-----
From: jmchil...@gmail.com [mailto:jmchil...@gmail.com] On Behalf Of John Chilton
Sent: Tuesday, 23 October 2012 7:59 AM
To: Jorrit Boekel
Cc: Khassapov, Alex (CSIRO IM&T, Clayton)
Subject: Re: Fwd: [galaxy-dev] pass more information on a dataset merge

Hello again Jorrit,

Great, I am glad we are largely on the same page here. I don't know when I will 
get a chance to look at this particular aspect, if you get there first that 
will be great, if not I will get there eventually.

-John

On Mon, Oct 22, 2012 at 2:51 AM, Jorrit Boekel <jorrit.boe...@scilifelab.se> 
wrote:
> IIRC, I implemented the task_X suffix (galaxy does so as well but to
> the split subdirectories) to ensure jobs that contained multiple split
> datasets would be run in sync. Files from two datasets that belong
> together then get analysed together in subsequent steps.
>
> It would however be much nicer to retain original file names through a
> pipeline or at least the possibility to retrieve them. Since the
> split/merge now run actively look and match for files with identical
> 'task_x', it may be an option to do:
>
> fraction1.raw -> fraction1.raw_dataset_43.dat_task_0 ->
> fraction1.raw_dataset_44.dat_task_0
> fraction2.raw -> fraction2.raw_dataset_43.dat_task_1 ->
> fraction2.raw_dataset_44.dat_task_1
>
> (Note that python starts counting at 0, while most researchers number
> their first fraction 1.)
>
> I wouldn't mind looking more into that as well, since it would be a
> big improvement UI-wise.
>
> cheers,
> jorrit
>
>
>
>
>
>
> On 10/19/2012 04:40 PM, John Chilton wrote:
>>
>> Jorrit I meant to cc you on this response to Alex.
>>
>> ---------- Forwarded message ----------
>> From: John Chilton <chil0...@umn.edu>
>> Date: Fri, Oct 19, 2012 at 9:40 AM
>> Subject: Re: [galaxy-dev] pass more information on a dataset merge
>> To: alex.khassa...@csiro.au
>>
>>
>> Hey Alex,
>>
>> I think the idea here is that your initially uploaded files would
>> have different names, but after Jorrit's tool split/merge step they
>> will all just be named after the dataset id (see screenshot) so you
>> need the task_X at the end so they don't all just have the same name.
>>
>> I have not thought a whole lot about the naming thing, in general it
>> seems like a tough problem and one that Galaxy itself doesn't do a
>> particularly good job at.
>>
>> Jorrit have you given any thought to this?
>>
>> I wonder if it would be feasible to use the initial uploaded name as
>> a sort of prefix going forward. So if I upload say
>>
>> fraction1.RAW
>> fraction2.RAW
>> fraction3.RAW
>>
>> and run a conversion step, maybe I could get:
>>
>> fraction1_dataset567.ms2
>> fraction2_dataset567.ms2
>> fraction3_dataset567.ms2
>>
>> instead of
>>
>> dataset567.dat_task_0
>> dataset567.dat_task_1
>> dataset567.dat_task_2
>>
>> Jorrit do you mind if I give implementing that a shot? It seems like
>> it would be a win to me. Am I am going to hit some problem I don't
>> see now (presumable we have to send some data from the split to the
>> merge and that might be tricky)?
>>
>> -John
>>
>> On Thu, Oct 18, 2012 at 7:00 PM,  <alex.khassa...@csiro.au> wrote:
>>>
>>> Thanks John,
>>>
>>> I wonder what's the reason for appending _task_XX to the file names,
>>> why can't we just keep original file names?
>>>
>>> Alex
>>>
>>> -----Original Message-----
>>> From: jmchil...@gmail.com [mailto:jmchil...@gmail.com] On Behalf Of
>>> John Chilton
>>> Sent: Friday, 19 October 2012 6:16 AM
>>> To: Khassapov, Alex (CSIRO IM&T, Clayton)
>>> Subject: Re: [galaxy-dev] pass more information on a dataset merge
>>>
>>> On Tue, Oct 16, 2012 at 11:11 PM,  <alex.khassa...@csiro.au> wrote:
>>>>
>>>> Hi John,
>>>>
>>>> I am definitely interested in this idea, not only me - we are
>>>> currently working on moving a few scientific tools (not related to
>>>> genome) into cloud using Galaxy.
>>>
>>> Great. My interests in Galaxy are mostly outside of genomics as
>>> well, it is good to have more people utilizing Galaxy in this way
>>> because it will force the platform to become more generic and
>>> address more broader use cases.
>>>
>>>> We will try it further and see if we need any changes. For now one
>>>> improvement would be nice, make dataset_id.dat contain list of
>>>> paths to the location of the uploaded files, so by displaying html
>>>> page the user could just click on the link and download the file.
>>>>
>>> Code that attempted to do this was in there, but didn't work
>>> obviously. I have now fixed it up.
>>>
>>> Thanks for beta testing.
>>>
>>> -John
>>>
>>>> We are pretty new to Galaxy, so our understanding of Galaxy is
>>>> pretty limited.
>>>>
>>>> Thanks again,
>>>>
>>>> Alex
>>>>
>>>>
>>>> -----Original Message-----
>>>> From: jmchil...@gmail.com [mailto:jmchil...@gmail.com] 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,  <alex.khassa...@csiro.au> 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/grouping.py 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(
>>>>> trans.app.config.ftp_upload_dir, trans.user.email )" throws an exeption 
>>>>> if ftp_upload_dir isn't set.
>>>>>
>>>>> Alex
>>>>>
>>>>> -----Original Message-----
>>>>> From: galaxy-dev-boun...@lists.bx.psu.edu
>>>>> [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of John
>>>>> Chilton
>>>>> Sent: Tuesday, 16 October 2012 1:07 AM
>>>>> To: Jorrit Boekel
>>>>> Cc: galaxy-dev@lists.bx.psu.edu
>>>>> 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.
>>>>>
>>>>> https://bitbucket.org/galaxyp/galaxy-central-homogeneous-composite
>>>>> -da
>>>>> t
>>>>> 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: https://bitbucket.org/jmchilton
>>>>> Github: https://github.com/jmchilton
>>>>> Web: http://jmchilton.net
>>>>>
>>>>> On Mon, Oct 8, 2012 at 9:24 AM, John Chilton <chil...@msi.umn.edu>
>>>>> 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:
>>>>>>
>>>>>> https://bitbucket.org/galaxy/galaxy-central/pull-request/76/multi-input-data-tool-parameter-fixes).
>>>>>>
>>>>>> 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: https://bitbucket.org/jmchilton
>>>>>> Github: https://github.com/jmchilton
>>>>>> Web: http://jmchilton.net
>>>>>>
>>>>>> On Mon, Oct 1, 2012 at 8:24 AM, Jorrit Boekel
>>>>>> <jorrit.boe...@scilifelab.se> 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
>>>>>>>
>>>>>>> ___________________________________________________________
>>>>>>> Please keep all replies on the list by using "reply all"
>>>>>>> in your mail client.  To manage your subscriptions to this and
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>>>>>>>   http://lists.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
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>>>>>
>>>>>    http://lists.bx.psu.edu/
>
>
>
> --
> Scientific programmer
> Mass spec analysis support @ BILS
> Janne Lehtiö / Lukas Käll labs
> SciLifeLab Stockholm
>

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