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<mailto: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(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@illumina.com<mailto:jduddy@illumina.com>
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Greg Von Kuster
Galaxy Development Team
greg@bx.psu.edu<mailto:greg@bx.psu.edu>