Hey Marco,

Thanks for the e-mail. This is an awesome idea, but I am worried it is
very hard to do this well in Galaxy. If you create symbolic links to
the original file - then Galaxy might delete the original file and the
derived files would all break without warning. Galaxy does have this
separate concept of datasets and history dataset associations so that
a dataset can exist in more than one place simultaneously - and one
could imagine sticking this metadata there and just sort of
dynamically splitting up the BAM file whenever it is used in a tool or
served out over the API - but this would be a large effort and would
require all sorts of modifications to various parts of Galaxy.

Something worth looking at is this work by Kyle Ellrott:

https://bitbucket.org/galaxy/galaxy-central/pull-request/175/parameter-based-bam-file-parallelization

This was a very localized effort to just work some of the ideas just
into the task splitting framework in Galaxy. This has the advantage of
not needing to mess with metadata and datasets, etc.... all the way up
the chain.

Kyle has abandoned that approach however, but it is promising start to
something like this I think - and it would be much less disruptive
than doing this with metadata and datasets (though admittedly more
limited as well).

If this will be primarily used for workflows - there are a couple of
recent developments that might make splitting more feasible. Dannon
introduced the ability to delete intermediate outputs from workflows a
few releases ago - and the upcoming release (15.03) will introduce the
ability to write tools that split up a single input into a collection.
The existing workflow and dataset collection framework can then apply
normal tools over every element of the collection and you can write a
tool to merge the results. More information can be found here -
https://bitbucket.org/galaxy/galaxy-central/pull-request/634/allow-tools-to-explicitly-produce-dataset.

These common pipelines where you split up a BAM files, run a bunch of
steps, and then merge the results will be executable in the near
future (though 15.03 won't have workflow editor support for it - I
will try to get to this by the following release - and you can
manually build up workflows to do this -
https://bitbucket.org/galaxy/galaxy-central/src/0468d285f89c799559926c94f300c42d05e8c47a/test/api/test_workflows.py?at=default#cl-544).

Thanks again,
-John


On Fri, Feb 27, 2015 at 10:04 PM, Marco Albuquerque
<marcoalbuquerque....@gmail.com> wrote:
> Hello Galaxy Dev,
>
> I have a question regarding parallelism on a BAM file.
>
> I have currently implemented 3 split options for the BAM datatype
>
> 1) by_rname -> splits the bam into files based on the chromosome
> 2) by_interval -> splits the bam into files based on  a defined bp length,
> and does so across the entire genome present in the BAM file
> 3) by_read -> splits the bam into files based on the number of reads
> encountered (if multiple files, all other files match the interval as the
> first)
>
> Now, as you can imagine, reading and writing large BAM files is a pain, and
> I personally think this is not the best solution for Galaxy.
> What I was hoping to implement (but don't know how) is to create a new
> metadata option in bam (bam.metadata.bam_interval) which would generate the
> interval without creating a new file (essentially, I would create a symbolic
> link to the old large file, and then update the metadata.bam_interval, this
> would contain some string of the form chrom:start-end which could then be
> used in a variety of tools which accept an interval as an option (for
> example samtools view))
>
> This would be far more efficient then my first implementation, but the thing
> I don't know how to do is specify some kind of metadata at the split level.
> I was hoping maybe you could direct me to an example that does this?
>
> I have added the following to my metadata.py file:
>
> class IntervalParameter( MetadataParamter )
>
>     def __init__( self, spec ):
>         MetadataParamter.__init__( self, spec ):
>         self.rname = self.spec.get( "rname" )
>         self.start = self.spec.get( "start" )
>         self.end = self.spec.get( "end" )
>
>     def to_string(self):
>         if self.rname = 'all':
>             return ''
>         else:
>             return ''.join([self.rname, ':', self.start, '-', self.end])
>
> And the following to my binary.py file:
>
> ### UNDER THE BAM CLASS
>
> MetadataElement( name="bam_interval", desc="BAM Interval",
> param=metadata.IntervalParameter, rname="all", start="", end="",
> visible=False, optional=True)
>
>
> I somehow want rname="all" to be the default, but upon parallelism, I want
> to be able to adjust this parameter in the split functions.
>
> So,
>
> <parallelism method="multi" split_inputs="normal,tumour"
> split_mode="by_interval" split_size="50000000" merge_outputs="output"/>
>
> Would actually change the metadata of each file, and not create sub-bams.
>
>
> PLEASE HELP!!!
>
> Marco
>
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