Hi John, Thanks for your reply.
I think for the time being, I will simply create a tool that creates an interval file, and the parallelize on this interval file. Though I agree, this would be a useful feature to include but I don't think I am anywhere near ready to start dabbling in galaxy's core filesystem as I have only been developing for a short while. Im hoping that I can learn more about how galaxy works at the GCC, and maybe then I will know how to efficiently adjust galaxy code. I am actually hoping to present my work at the GCC15, I am part of a project that is adding a variety of Cancer Genomic Tools into galaxy. And thanks so much for the resources, I will surely look into all of these. Much appreciated, Marco On 2015-03-02 9:22 AM, "John Chilton" <jmchil...@gmail.com> wrote: >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-bas >ed-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-t >o-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/0468d285f89c799559926c94f3 >00c42d05e8c47a/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 >> >> ___________________________________________________________ >> Please keep all replies on the list by using "reply all" >> in your mail client. 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