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: jdu...@illumina.com<mailto:jdu...@illumina.com>

From: Greg Von Kuster [mailto:g...@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: jdu...@illumina.com<mailto:jdu...@illumina.com>

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Greg Von Kuster
Galaxy Development Team
g...@bx.psu.edu<mailto:g...@bx.psu.edu>



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