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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