Peter Cock wrote:
> On Tue, Sep 6, 2011 at 3:24 PM, Nate Coraor <> wrote:
> > Edward Kirton wrote:
> >> Peter wrote:
> >> > 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
> Yes, that's what I was envisioning Nate.
> Are there any schemes other than gzip which would make sense?
> Perhaps rather than a boolean column (compressed or not), it
> should specify the kind of compression if any (e.g. gzip).

Makes sense.

> We need something which balances compression efficiency (size)
> with decompression speed, while also being widely supported in
> libraries for maximum tool uptake.

Yes, and there's a side effect of allowing this: you may decrease
efficiency if the tools used downstream all require decompression, and
you waste a bunch of time decompressing the dataset multiple times.


> Peter
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