On Tue, Sep 6, 2011 at 5:12 PM, Nate Coraor <n...@bx.psu.edu> wrote:
> Peter Cock wrote:
>> On Tue, Sep 6, 2011 at 5:00 PM, Nate Coraor <n...@bx.psu.edu> wrote:
>> > Peter Cock wrote:
>> >> On Tue, Sep 6, 2011 at 3:24 PM, Nate Coraor <n...@bx.psu.edu> wrote:
>> >> > 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.
>>
>> While decompression wastes CPU time and makes things slower,
>> there is less data IO from disk (which may be network mounted)
>> which makes things faster. So overall, depending on the setup
>> and the task at hand, it could be faster.
>>
>> Is it time to file an issue on bitbucket to track this potential
>> enhancement?
>
> Sure.
>

Issue filed, better late than never:
https://bitbucket.org/galaxy/galaxy-central/issue/666/

This was prompted by another thread where gzipped FASTQ
was proposed:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-October/007069.html

Peter
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