GATK2 (from IUC) Missing reference_genome selection
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: geert.vandeweyer@ua.ac.be http://ua.ac.be/cognitivegenetics http://www.linkedin.com/in/geertvandeweyer
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
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participants (2)
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Björn Grüning -
Geert Vandeweyer