On Thu, Oct 6, 2011 at 3:48 PM, Duddy, John <jduddy(a)illumina.com> wrote:
I'd be up for that something like that, although I have other
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.