GATK2 (from IUC) Missing reference_genome selection

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GATK2 (from IUC) Missing reference_genome selection

Geert Vandeweyer-4
Hi,

I'm using the GATK2 tools from IUC, taken from the main toolshed. After
configuration, I'm able to run the tools as standalone jobs, and
everything works.

When I add the job to a workflow, The 'Using reference genome' selection
is empty (see screenshot in attachment for PrintReads tool). Just
filling in the database key (hg19 in my case) allows the workflow to run
correctly.

When I noticed that the Unified Genotyper does not show this behaviour,
I checked the XML files. After commenting out the following line (which
is commented in Unified Genotyper by default) in the "Realigner Target
Creator" tool, The selection drop-down menu showed correctly for RTC:

<filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/>


So I assume that this filter is conflicting with the workflow editor
somehow. Is this an issue on my site only, or is this a general bug?

On a side note: i'd like to be able to set the java --max_jvm_heap value
on a per-gatk-tool basis without directly editing the xml files, instead
of using the default heap_fraction setting. Is this possible (yet) ?
Editing the XML files caused the update of toolshed_packages to fail by
launching interactive diff-merge tasks when updating from the website.

Kind regards,

Geert


--

Geert Vandeweyer, Ph.D.
Department of Medical Genetics
University of Antwerp
Prins Boudewijnlaan 43
2650 Edegem
Belgium
Tel: +32 (0)3 275 97 56
E-mail: [hidden email]
http://ua.ac.be/cognitivegenetics
http://www.linkedin.com/in/geertvandeweyer


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Re: GATK2 (from IUC) Missing reference_genome selection

Björn Grüning-3
Hi Geert,


> Hi,
>
> I'm using the GATK2 tools from IUC, taken from the main toolshed. After
> configuration, I'm able to run the tools as standalone jobs, and
> everything works.
>
> When I add the job to a workflow, The 'Using reference genome' selection
> is empty (see screenshot in attachment for PrintReads tool). Just
> filling in the database key (hg19 in my case) allows the workflow to run
> correctly.
>
> When I noticed that the Unified Genotyper does not show this behaviour,
> I checked the XML files. After commenting out the following line (which
> is commented in Unified Genotyper by default) in the "Realigner Target
> Creator" tool, The selection drop-down menu showed correctly for RTC:
>
> <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/>
>
>
> So I assume that this filter is conflicting with the workflow editor
> somehow. Is this an issue on my site only, or is this a general bug?

Its a general issue, and I think its also a bug. That filter step should
ensure that the genome dbkey from vcf and bam are identical. But it
seems that the workflow editor is not supporting it. I had a look at
bowtie2 and it seems bowtie2 also do not use that filter.

If you like you can fill a trello card with that issue and please a PR to:

https://github.com/bgruening/galaxytools for the GATK tools.

> On a side note: i'd like to be able to set the java --max_jvm_heap value
> on a per-gatk-tool basis without directly editing the xml files, instead
> of using the default heap_fraction setting. Is this possible (yet) ?
> Editing the XML files caused the update of toolshed_packages to fail by
> launching interactive diff-merge tasks when updating from the website.

No that is currently not supported, at least not for every single tool,
you can do that for all GATK tools if you like. I think we have a trello
card for that feature request. Please upvote it :)

Thanks for using the GATK wrappers and reporting these issues.
Bjoern

> Kind regards,
>
> Geert
>
>
>
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>    http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>    http://galaxyproject.org/search/mailinglists/
>
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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To search Galaxy mailing lists use the unified search at:
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