easier iRODS publish for realignment results

[dkj]

This is not critical as I have worked around the problems encountered. Using this issue to note down a few minor pain points to potentially inform future development (so not a priority but if code needed reworking for some other reason...).

I was trying to upload realignment results (plex level data) from S3 into iRODS. I made the S3 results bucket available as a filesystem using s3fs. To reduce metadata lookups I created another fs hierarchy which symlinked into the s3fs for cram and associated auxiliary files. I'd have liked:

• to avoid reliance on flagstats json files (not 100% sure of this requirement - possible PEBCAK) - I had not created these
• to avoid reliance on RunInfo.xml and runParameters.xml files - I downloaded these from iRODS into the shadow hierarchy (and specified --runfolder-path as well as --archive-path)
• easier stack trace access (to help figure out the above xml file dependency) - my usual magic of perl -MCarp=verbose had no effect (--debug was specified)
• (v minor) to specify the samtools command (set to samtools_irods) on the command line (as I had for the realignment tool) - I just created a suitable symlink
• (not at all sure) some alias option or realign cleverness to shortcut --no-xml, --no-qc and --no-interop

[dkj]

and #108 ...