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. 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. 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 ;-} John Duddy Sr. Staff Software Engineer Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Tel: 858-736-3584 E-mail: jduddy@illumina.com -----Original Message----- From: Peter Cock [mailto:p.j.a.cock@googlemail.com] Sent: Thursday, October 06, 2011 1:28 AM To: Duddy, John Cc: Greg Von Kuster; galaxy-dev@lists.bx.psu.edu; Nate Coraor Subject: Re: [galaxy-dev] Tool shed and datatypes On Thu, Oct 6, 2011 at 4:48 AM, Duddy, John <jduddy@illumina.com> wrote:
One of the things we're facing is the sheer size of a whole human genome at 30x coverage. An effective way to deal with that is by compressing the FASTQ files. That works for BWA and our ELAND, which can directly read a compressed FASTQ, but other tools crash when reading compressed FASTQ filesfiles. One way to address that would be to introduce a new type, for example "CompressedFastQ", with a conversion to FASTQ defined. BWA could take both types as input. This would allow the best of both worlds - efficient storage and use by all existing tools.
We'd discussed this and a more general approach where any file could be gzipped, but the code to do that doesn't exist yet: http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-September/006745.html Issue filed: https://bitbucket.org/galaxy/galaxy-central/issue/666/ That seems a better long term solution than the pragmatic short term solution of fastqsanger-gzip (or whatever it gets called). Note that it sounded like Edward Kirton might already be using this - you should be consistent. The other strong idea from that thread was moving from FASTQ to unaligned BAM, which is gzipped compressed, and has explicit support for paired end reads, read groups, etc. Peter