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: ralonso@cipf.es