On 10/25/2012 11:25 AM, Peter Cock wrote:
On Thu, Oct 25, 2012 at 10:00 AM, Jorrit Boekel
<jorrit.boe...@scilifelab.se> wrote:
On 10/25/2012 10:54 AM, Peter Cock wrote:
On Thu, Oct 25, 2012 at 9:36 AM, Jorrit Boekel
<jorrit.boe...@scilifelab.se> wrote:
Dear list,

In my galaxy fork, I extensively use the job splitters. Sometimes though,
have to split to different file types for the same job. That raises an
exception in the lib/galaxy/jobs/splitters/multi.py module.

I have turned this behaviour off for my own work, but am now wondering
whether this is very bad practice. In other words, does somebody know why
the multi splitter does not support multiple file type splitting?

Could you clarify what you mean by showing some of your tool's XML
file. i.e. How is the input and its splitting defined.

Are you asking about splitting two input files at the same time?


Hi Peter,

Something like the following:

  <command interpreter="python">bullseye.py $hardklor_results
$ms2_in.extension $ms2_in $output $use_nonmatch</command>
  <parallelism method="multi" split_inputs="hardklor_results,ms2_in"
shared_inputs="config_file" split_mode="from_composite"

The tool takes two datasets of different formats, which are to be split in
the same amount of files, which belong together as pairs.
So the inputs are $hardklor_results and $ms2_in (which should be split
in a paired manor) and there is one output $output to merge?

What is shared_inputs="config_file" for as that isn't in the
<command> tag anywhere.
Exactly. The tool uses results from a tool called hardklor to adjust the mass spectra contained in the ms2_input. And whoops, haven't taken out the now obsolete config file. thanks for spotting that.

Note that I have implemented an odd way of splitting, which is from a number
of files in the dataset.extra_files_path to symlinks in the task working
dirs. The number of files is thus equal to the number of parts resulting
from a split, and I have ensured that each part is paired correctly. I
assume this hasn't been necessary in the genomics field, but for proteomics,
at least in our lab, multiple-file datasets are the standard.

My fork is at http://bitbucket.org/glormph/adapt if you want to check more
I don't quite follow your example, but I can see some (simpler?) cases
for sequencing data - paired splitting of a FASTA + QUAL file, or
paired splitting of two FASTQ files (forward and reverse reads). Here
the sequence files can be broken up into any size (e.g. split in four,
or divided into batches of 10000, but not split based on size on disk),
as long as the pairing is preserved.

i.e. Given FASTA and QUAL for read1, read2, ...., read100000 then
if the FASTA file is split into read1, read2, ...., read1000 as the first
chunk, then the first QUAL chunk must also have the same one
thousand reads.

(In these examples the pairing should be verifiable via the read
names, so errors should be easy to catch - I don't know if you have
that luxury in your situation).

What you describe is pretty much the same as my situation, except that I don't have two large single input files as your fastq files, but two sets of the same number of files stored in the composite file directories (galaxy/database/files/000/dataset_x_files ). I keep the files matched by keeping a _task_%d suffix to their names. So each task is matched with its correct counterpart with the same number.

My question is still though if it would be bad to not raise an exception when different filetypes are split in the same job.


Scientific programmer
Mass spec analysis support @ BILS
Janne Lehtiö / Lukas Käll labs
SciLifeLab Stockholm

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