Alex,

To reiterate what Jeremy has already said on the mailing list, this is
definitely something we want, and need, for Galaxy.  While this particular
implementation has a lot of good parts, creating these collections as
first-class composite datasets isn't ideal and we'd be stuck supporting
them going forward, forever.

There's a clear plan for implementing this in Trello (
https://trello.com/c/325AXIEr), most of which is straightforward to
implement.  The 'hard' part is really going to be implementing an ideal UI
for dealing with these collections, something which we could do in phases.

What exactly are your concerns with the implementation as set out in the
Trello card?

-Dannon



On Mon, Mar 4, 2013 at 1:32 AM, <alex.khassa...@csiro.au> wrote:

> Yeah John,
>
> This is sad, I don't understand why it is such a problem? If it's already
> implemented and used in real projects like ours - then it is needed for the
> community.  I don't think we have other options for our requirements, your
> multiple file datasets implementation was a real saviour for us.
>
> -Alex
>
> -----Original Message-----
> From: jmchil...@gmail.com [mailto:jmchil...@gmail.com] On Behalf Of John
> Chilton
> Sent: Monday, 4 March 2013 4:42 PM
> To: Khassapov, Alex (CSIRO IM&T, Clayton)
> Cc: <galaxy-...@bx.psu.edu>
> Subject: Re: [galaxy-dev] Composite datatype output for Cuffdiff
>
> Hi Alex,
>
>   Thanks for the comments. The galaxy team has made it clear here and to
> me privately that this will NOT be included in the Galaxy main code base. I
> hope and am I confident that they will make grouping datasets work,
> hopefully even to thousands of files.
>
>   I do not believe the two ideas are mutually exclusive and I will be
> maintaining a fork of galaxy-central with these additions, I will set this
> up this week hopefully. I will do my best to respond to support requests
> and make multiple file datasets and composite types in general as robust as
> possible, keep up with Galaxy updates, etc....
> Obviously, it is risky to let a code base drift so far from galaxy main's
> however and you, me, and others who might want to use them will have to
> carefully weigh the risks when determining if multiple file datasets are
> worth the headache.
>
>   Thanks for all your help and inputs. I am sorry this did not turn out
> differently, I feel I have really failed here.
>
> -John
>
>
> On Sun, Mar 3, 2013 at 10:08 PM,  <alex.khassa...@csiro.au> wrote:
> > Hi John,
> >
> > Are you saying that "composite multiple file dataset" isn't required and
> won't be implemented?
> >
> > We are using your implementation of multifiles dataset ("m:xxx" type)
> and hope that eventually it will be pushed into main Galaxy implementation.
> >
> > As we are using Galaxy for CT reconstruction tools, where input and
> output can consist of a couple thousand files, other options are not
> feasible, i.e. grouping datasets.
> >
> > -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: Thursday, 28 February 2013 2:06 AM
> > To: Jeremy Goecks
> > Cc: Jim Johnson; <galaxy-...@bx.psu.edu>
> > Subject: Re: [galaxy-dev] Composite datatype output for Cuffdiff
> >
> > Hey Jeremy,
> >
> >   I am trying to think about a path forward with this composite multiple
> file dataset implementation. It seems there is consensus among the galaxy
> team that it shouldn't be included because grouping actual datasets would
> be superior. In that light, I am revisiting this e-mail, because depending
> on the implementation of what you described multiple file datasets are a
> specific case of this concept with some likely uncontroversial enhancements
> for the specific case of composite datatypes that are a homogeneous list of
> files. Does that make any sense?
> >
> >   If I implemented (i) and (ii) in such a way that the multiple file
> dataset stuff flowed out more organically is there any chance than it could
> be included in galaxy-central. If no and the implicit datatypes and
> parallelism stuff would remain no-gos implementing what you described would
> still benefit the multiple file datasets implementation, so I still might
> do this, would a clean implementation of just what you described be
> accepted?
> >
> >   Any thoughts you or anyone has on the future direction of composite
> datatypes in general would be appreciated?
> >
> > Thanks for your time,
> > -John
> >
> >
> > On Fri, Oct 12, 2012 at 2:44 PM, Jeremy Goecks <jeremy.goe...@emory.edu>
> wrote:
> >> Hi Jim,
> >>
> >> This is nice and is a path forward for the immediate future.
> >>
> >> That said, a couple extensions to Galaxy to better support composite
> >> datatypes would enable cummerbund without the additional tools:
> >>
> >> (i) extending the composite datatype to include definition of
> >> individual outputs in the collection;
> >> (ii) extend the history panel to allow usage/selection of (1) the
> >> complete composite set of files or (2) individual items in a
> >> composite datatype
> >>
> >> Once (i) is done, (ii) should be straightforward using the new
> >> history panel code.
> >>
> >> Of course, the advantage of these extensions is that they'd address
> >> both cummerbund issues as well as other challenges, such as using
> >> output from the barcode splitter.
> >>
> >> J.
> >>
> >> On Oct 11, 2012, at 6:14 PM, Jim Johnson wrote:
> >>
> >> Checking to see if there is any interest in including a parameter
> >> option to select outputs for cuffdiff, potentially including a
> >> composite output and a cummeRbund sqlite database.
> >>
> >> Issues:
> >>   cuffdiff produces 21 output files, which is a little unwieldy in a
> >> galaxy history.
> >>   cummeRbund generates its database when given a cuffdiff output
> >> directory, but manually hooking up 21 outputs to the cummerbund_wrapper
> is a pain.
> >>
> >> I've put demo code in the testtoolshed under the name repository name
> >> cummerbund
> >>
> >> http://jjohn...@testtoolshed.g2.bx.psu.edu/repos/jjohnson/cummerbund
> >>
> >> This includes new datatypes defined in datatypes_conf.xml and
> >> implemented in
> >> cuffdata.py:
> >>       <!-- html composite dataset with cuffdiff outputs in the extra
> >> files path -->
> >>       <datatype extension="cuffdata"
> >> type="galaxy.datatypes.cuffdata:CuffDiffData"/>
> >>       <!-- cummeRbund SQLite database -->
> >>       <datatype extension="cuffdatadb"
> >> type="galaxy.datatypes.cuffdata:CuffDataDB"/>
> >>
> >> The cuffdiff wrapper has a multiple select parameter to choose which
> >> output files to put in the history.
> >> In addition to the 21 cuffdiff outputs, the wrapper can also generate:
> >>   cuffdata - which is a composite HTML output with links to the 21
> >> cuffdiff outputs
> >>   cuffdatadb - which is the cummeRbund SQLite database
> >>
> >> I also added utility tools:
> >>   cuffdata_datasets - which will take files from the composite
> >> cuffdata and copy them as datasets into the history
> >>   cuffdata_cummerbund - which generates the cummeRbund cuffdatadb
> >> from the composite cuffdata
> >>
> >> I updated the cummerbund_wrapper:
> >>   with tryCatch so that a R error on a plot won't exit the Rscript
> >>   to include a small image of each plot on the html page
> >>   added plots for : dispersion, scatter matrix, MDS, and PCA
> >>
> >> Thanks,
> >> JJ
> >>
> >>
> >>
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