Edward Kirton wrote:
> > In your position I agree that is a pragmatic choice.
> 
> Thanks for helping me muddle through my options.
> 
> > You might be able to
> > modify the file upload code to gzip any FASTQ files... that would prevent
> > uncompressed FASTQ getting into new histories.
> 
> Right!
> 
> > I wonder if Galaxy would benefit from a new fastqsanger-gzip (etc) datatype?
> > However this seems generally useful (not just for FASTQ) so perhaps a more
> > general mechanism would be better where tool XML files can say which file
> > types they accept and which of those can/must be compressed (possily not
> > just gzip format?).
> 
> Perhaps we can flesh-out what more general solutions would look like...
> 
> Imagine the fastq datatypes were left alone and instead there's a
> mechanism by which files which haven't been used as input for x days
> get compressed by a cron job.  the file server knows how to uncompress
> such files on the fly when needed.  For the most part, files are
> uncompressed during analysis and are compressed when the files exist
> as an archive within galaxy.

Ideally, there'd just be a column on the dataset table indicating
whether the dataset is compressed or not, and then tools get a new
way to indicate whether they can directly read compressed inputs, or
whether the input needs to be decompressed first.

--nate

> 
> An even simpler solution would be an archive/compress button which
> users could use when they're done with a history.  Users could still
> copy (uncompressed) datasets into a new history for further analysis.
> 
> Of course there's also the solution mentioned in the 2010 galaxy
> developer's conference about automatic compression at the system
> level.  Not a possibility for me, but is attractive.
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