Hi Alex and Peter,

  I appreciate the comments, but I am not going to keep talking about
this issue here, I consider the issue closed. The Galaxy team has
spoken clearly on this topic. They have accepted dozens of my pull
requests and I am very happy about all of them, and I need them to
accept dozens (if not hundreds) more in the future so I cannot afford
to continue to burn political capital by talking about this in this

  Alex, I plan to support some version of multiple file datasets for
at least the next two years. I will put the code here when it is ready
- https://bitbucket.org/msiappdev/galaxy-extras. Peter, I have
responded to your questions here -


On Mon, Mar 4, 2013 at 4:49 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> Hi all,
> I've retitled this from "Composite datatype output for Cuffdiff" to
> "Implementing dataset collections" to try and link into Jeremy's thread.
> References:
> http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-February/013574.html
> http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-March/013634.html
> http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-March/013636.html
> On Mon, Mar 4, 2013 at 4:08 AM,  <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
> On Mon, Mar 4, 2013 at 5:42 AM, John Chilton <chil...@msi.umn.edu> wrote:
>> 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
> Hi John,
> Does your multiple file system work on composite datatypes? For
> example, given a 'blastdbn' file (several files making up a BLAST
> nucleotide database) could we use 'm:blastdbn' to refer to several
> BLAST databases? Is this at least possible in principle based
> on your work so far?
> How different is your m:xxx grouping of multiple files of a given
> datatype at odds with the dataset collections idea as outlined by
> Jeremy Goecks here?
> http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-February/013574.html
> https://trello.com/c/325AXIEr
> Jeremy's idea mentions the special case of a unique dataset
> collection object for paired-end reads - well if that was defined
> using the existing core Galaxy functionality as a 'pairedfastq'
> composite datatype (made of two FASTQ files), then could we
> use 'm:pairedfastq' (with your enhancement) for a whole bunch
> of paired FASTQ files.  Nice? :)
> Regards,
> Peter
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