On Tue, Mar 25, 2014 at 11:42 AM, Hans-Rudolf Hotz wrote:
> Hi Brian
> It is difficult to imagine where such files are coming from. As each file in
> ~/database/files/*/ has a corresponding entry in the 'dataset' table.  If you
> have such files, then something went horribly wrong, eg by using two
> different databases on the same files system.  To double check manually
> compare the list of files on the file system, with the contents of the 
> 'dataset'
> table.
> Also, have a look at the ~/database/job_working_directory/ and
> ~/database/tmp/ directories. You might have some old, big files there
> using a lot of space.
> Regards, Hans-Rudolf

I think Brian is right - there is nothing to stop tools writing temp
files under ~/database/files/*/ - the most obvious examples would
be any index file named after the input dataset it is indexing
(e.g. like *.bai and *.fai files normally next to a *.bam or *.fasta).
Similarly file format conversions may also be generated next
to the input file (although here using $TMP seems preferable).

Tool/wrappers may or may not clean up this sort of thing, and
in the event of a job failure, stray files are more likely to remain.

So I agree, it would be good to have a script audit what Galaxy
thinks is under ~/database/files/*/ tracked in its database, and
what extra files have appeared.


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