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
