> 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.

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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