On Thu, Oct 6, 2011 at 3:48 PM, Duddy, John <jdu...@illumina.com> wrote:
> I'd be up for that something like that, although I have other tasking
> in the short term after I finish my parallelism work. I'd rather not have
> Galaxy do the compression/decompression, because that will not
> effectively utilize the distributed nature of many filesystems, such
> as Isilon, that our customers use.

Is that like a compressed filesystem, where there is probably less
benefit to storing the data gzipped?

> My parallelism work (second
> phase almost done) handles that by using a block-gzipped
> format and index files that allow the compute nodes to seek to
> the blocks they need and extract from there.

How similar is your block-gzipped approach to BGZF used in BAM?

> Another thing that should probably go along with this is an
> enhancement to metadata such that it can be fed in from the
> outside. We upload files by linking to file paths, and at that
> point, we know everything about the files (index information).
> So need to decompress a 500GB file and read the whole
> thing just to count the lines - all you have to do is ask ;-}

I can see how that might be useful.

Peter
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