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 <jmchilton@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
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> /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
On Thu, Apr 23, 2015 at 11:55 AM, Roberto Alonso CIPF <ralonso@cipf.es> wrote: 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: ralonso@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: ralonso@cipf.es