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How should we handle direct file access of files that we still want to do be handled by iRODS ?
Should we dig in to iRODS as ROOT
or still try the other way with non root user owning every vault fi…
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Using the glob on illumina_finished_msg, we should be able to checksum all the files after fastq generation and then check those on demand on other ends after the files have been transferred.
Thanks …
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The new tool-data config uses reference files in the biodata directory. Picard needs to create a dict file from the sequence file (e.g. hg19.fa). See function picard_index_ref in bcbio.broad.picardrun…
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$HOME among other env variables are not expanded correctly from the YAML files.