GenomicsDB on azure #8438
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GenomicsDB on azure #8438
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I see I didn't respond here previously, but this branch has been working for me and is what I'm currently using. Would be great to get it merged along with #8470 |
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Github actions tests reported job failures from actions build 7143483544
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* GATK's lack of support for az:// uri means that although genomicsdb can natively read them, parts of the java code crash when they're passed through * Adding --avoid-nio and --header parameters these allow disabling all of the java codes interaction with the az:// links and simply pass them through to genomicsdb This disables some safeguards but allows operating on files in azure * Move GenomicsDB version to released 1.5.1 for azure improved support * There are no direct tests on azure since we do not yet have any infrastructure to generate the necessary tokens --------- Co-authored-by: Nalini Ganapati <[email protected]> Co-authored-by: Nalini Ganapati <[email protected]>
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adding two new parameters which work together to allow passing through files from azure too genomicsDB
--header <vcf>which lets you specify a vcf file to use the header from as your merged header. Do not mess this up or you will likely be doomed.--avoid-niowhich disables GATK sanity checks that involve reading the files since this would require opening them on azure.This needs tests but I wanted to put it here for @meganshand to try.