Hi,
I have a couple of GATK issues
1. First is there a data manager for it? I have tried Generate GATK-sorted Picard indexes (data_manager_gatk_picard_index_builder) - builder and got no entries on the cached picard genomes.
2. With problem 1, we are using genomes from the history. It so happens that some XML files have the filtering of forcing the dbkey of the from-history genome to be the same as the BAM files (reduced below for easy reading):
<when value="history"> <param name="input_bam" type="data" format="bam"/> <param name="ref_file" type="data" format="fasta"> <options> <filter type="data_meta" key="dbkey" ref="input_bam" /> </options> </param> </when>
For example, here: https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/...
Now, this does not seem to work. I.e. when I make the dbkey of the BAM file and the FASTA file the same, the ref_file entry is still empty.
Also, some xml files have it, others do not.
As a temporary measure, I removed the options/filter in my local installation, but might this be a bug? Or is it a bug in my head?
Thanks, Tiago