Hello,

I have been reading those different threads  and I have some doubts that
you maybe can clarify me. In the thread you said: "ability to write tools
that split up a single input into a collection. ", I think this is focused
for workflows, but in any case, could we use this to split bams?
Another comment is the next:

"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 - "

As I was trying to write something that will do exactly this and I guess
there is someone working on this, do you think is it worth to continue
doing this or just switch to another thing? would you know the road-map of
this feature?

Thanks a lot,

Roberto

On 23 April 2015 at 20:09, John Chilton <jmchil...@gmail.com> wrote:

> I am a pragmatist - I have no problem just splitting the inputs and
> skipping the metadata files. I would just convert the error into an
> log.info() and warn that the tool cannot use metadata files. If the
> underlying tool needs an index it can recreate it instead I think. One
> can imagine a more intricate solution that would recreate metadata
> files as needed - but that would be a lot of work I think.
>
> Does that make sense?
>
> About BB PR 175 there were some recent discussions about that approach
> - I would check out
> http://dev.list.galaxyproject.org/Parallelism-using-metadata-td4666763.html
> .
>
> -John
>
> On Thu, Apr 23, 2015 at 11:55 AM, Roberto Alonso CIPF <ralo...@cipf.es>
> wrote:
> > Hello,
> > I ma trying ti write some code in order to give the possibility of
> > parallelize some tasks. Now, I was with the problem of splitting a bam in
> > some parts, for this I create this simple tool
> >
> > <parallelism method="multi" split_size="3" split_mode="number_of_parts"
> > merge_outputs="output" split_inputs="input" ></parallelism>
> >
> >   <command>
> >     java -jar
> > /home/ralonso/software/GenomeAnalysisTK-3.3-0/GenomeAnalysisTK.jar -T
> > UnifiedGenotyper -R /home/ralonso/BiB/Galaxy/data/chr_19_hg19_ucsc.fa -I
> > $input -o $output 2&gt; /dev/null;
> >
> >   </command>
> >   <inputs>
> >     <param format="bam" name="input" type="data" label="bam"/>
> >   </inputs>
> >   <outputs>
> >       <data format="vcf" name="output" />
> >   </outputs>
> >
> > But I have one problem, when I execute the tool it goes through this
> part of
> > code (I am working in dev branch):
> >
> > $galaxy/lib/galaxy/jobs/splitters/multi.py, line 75:
> >
> >     for input in parent_job.input_datasets:
> >         if input.name in split_inputs:
> >             this_input_files =
> > job_wrapper.get_input_dataset_fnames(input.dataset)
> >             if len(this_input_files) > 1:
> >                 log_error = "The input '%s' is composed of multiple
> files -
> > splitting is not allowed" % str(input.name)
> >                 log.error(log_error)
> >                 raise Exception(log_error)
> >             input_datasets.append(input.dataset)
> >
> > So, it is raising the exception because this_input_files=2, concretely:
> > ['/home/ralonso/galaxy/database/files/000/dataset_171.dat',
> >
> '/home/ralonso/galaxy/database/files/_metadata_files/000/metadata_13.dat'],
> > I guess that:
> > dataset_171.dat: It is the bam file.
> > metadata_13.dat: It is the bai file.
> >
> > So, Galaxy can't move on and I don't know which would be the best
> solution.
> > Maybe change the if to check only non-metadata files? I think I should
> use
> > both files in order to create the bam sub-files, but this would be inside
> > the Bam class, under binary.py file.
> > Could you please guide me before I mess things up?
> >
> > Thanks so much
> > --
> > Roberto Alonso
> > Functional Genomics Unit
> > Bioinformatics and Genomics Department
> > Prince Felipe Research Center (CIPF)
> > C./Eduardo Primo Yúfera (Científic), nº 3
> > (junto Oceanografico)
> > 46012 Valencia, Spain
> > Tel: +34 963289680 Ext. 1021
> > Fax: +34 963289574
> > E-Mail: ralo...@cipf.es
> >
> > ___________________________________________________________
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>



-- 
Roberto Alonso
Functional Genomics Unit
Bioinformatics and Genomics Department
Prince Felipe Research Center (CIPF)
C./Eduardo Primo Yúfera (Científic), nº 3
(junto Oceanografico)
46012 Valencia, Spain
Tel: +34 963289680 Ext. 1021
Fax: +34 963289574
E-Mail: ralo...@cipf.es
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