Can we introduce new file types via tools in the tool shed? It seems Galaxy can load them if they are in the datatypes configuration file. Does tool installation automate the editing of that file? John Duddy Sr. Staff Software Engineer Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Tel: 858-736-3584 E-mail: jduddy(a)illumina.com ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/

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.

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 ;-}

As I understand it, Isilion is built up from "bricks" that have storage and compute power. They replicate files amongst themselves, so that for every IO request there are multiple systems that could respond. They are interconnected by an ultra fast fibre backbone.

So, depending on your topology, it's possible to get a lot more throughput by working on different sections of the same file from different physical computers.

I haven't delved into BGZF, so I can't comment. My approach to block GZIP was just to concatenate multiple GZIP files and keep a record of the offsets and sequences contained in each. The advantage is compatibility, in that it decompresses just like it was one big chunk, yet you can compose subsets of the data without decompressing/recompressing and (as long as we actually have to write out the file subsets) can reap the reduced IO benefits of smaller writes.

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. Another example would be adding the CASAVA tools to Galaxy. Some of the statistics generation tools use custom file formats. To be able to make the use of those tools optional and configurable, they should be separate from the aligner, but that would require that Galaxy be made aware of the custom file formats – we’d have to add a datatype. John Duddy Sr. Staff Software Engineer Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Tel: 858-736-3584 E-mail: jduddy(a)illumina.com From: Greg Von Kuster [mailto:greg@bx.psu.edu] Sent: Wednesday, October 05, 2011 6:25 PM To: Duddy, John Cc: galaxy-dev(a)lists.bx.psu.edu Subject: Re: [galaxy-dev] Tool shed and datatypes Hello John, The Galaxy tool shed currently is not enabled to automatically edit the datatypes_conf.xml file, although I could add this feature if the need exists. Can you elaborate on what you are looking to do regarding this? Thanks! On Oct 5, 2011, at 1:52 PM, Duddy, John wrote: Can we introduce new file types via tools in the tool shed? It seems Galaxy can load them if they are in the datatypes configuration file. Does tool installation automate the editing of that file? John Duddy Sr. Staff Software Engineer Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Tel: 858-736-3584 E-mail: jduddy(a)illumina.com ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ Greg Von Kuster Galaxy Development Team greg(a)bx.psu.edu ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/

GZIP files are definitely our plan. I just finished testing the code that distributes the processing of a FASTQ (or pair for PE) to an arbitrary number of tasks, where each subtask extracts just the data it needs without reading any of the file it does not need. It extracts the blocks of GZIPped data into a standalone GZIP file just by copying whole blocks and appending them (if the window is not aligned perfectly, there is additional processing). Since the entire file does not need to be read, it distributes quite nicely. I'll be preparing a pull request for it soon. John Duddy

It's not public yet, and it involves a little conundrum - we want it so we can support large amounts of data efficiently on a variety of aligners, including our ELAND from CASAVA. However, ELAND does not support unaligned BAM inputs yet, and apparently it would be a lot of work to make it so (and another team's area of responsibility as well).

So in the near term, BGZF would not meet our needs.

However, work is quite far along on a GZIP-based one that works with ELAND and BWA, since they both read GZIP FASTQ files, and works/will work with a converter to fastq_sanger for other tools. I can put you in touch with the engineer doing the work if you are interested.