Whenever we try to load BAM files without copying them, we get an
stating the files need grooming, and can't use them at all.
Is it this serious? Would there be a way to bypass that?
Would you be able to help with a bit more detail and testing? #2
like it may be the issue, but without knowing more right now, I'll
provided the next troubleshooting steps.
1 - this is in your own install and it is current with the latest
or are you using -central (which pull?). Did something change between
the last successful BAM load and the new problem?
2 - "without copying" them means maybe that you are using a symbolic
link at your own site? This "load" is into a Library (this is how to
move data transferred outside of the Galaxy mechanisms into a history,
i.e. around a local file system by direct copy or similar). Load into
Library first, then copy to history. Instruction in wiki here:
3 - or do you mean "without copying" by using the FTP method set up
locally, followed by a load into a history?
4 - BAM file metadata (pencil icon -> Edit options) looks OK? Or, this
is the problem?
5 - SAMTools is loaded into your instance? Tools function on other BAM
files or all? Some simple SAMTools commands (that work with BAM files)
function line command OK on these (to rule out problem with BAM files
themselves - missing .bai index could be a problem).
6 - if you start with the same data and convert SAM->BAM within
does the SAM load and is the resulting BAM file OK?
7 - If you load the BAM file at the public Galaxy web site (using
the load is successful and the BAM file once imported into a history
appears OK? Please share link from this test in case we need to
(Options -> Share or Publish, generate link, email to me and I can
with dev team if needed).
Thanks for providing more info or perhaps you will find that one of
these uncovers the issue,