Re: [galaxy-dev] Tool shed and datatypes

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> ___________________________________________________________ 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@bx.psu.edu<mailto:greg@bx.psu.edu>