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@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@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@illumina.com
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