[galaxy-user] Help to identify variants with clinical/phenotype associations

[Luis Santomé]

Hi all,

I have a dataset with potential pathological variants and I'd like to
combine them to a dataset with known clinical association variants to
identify those responsible for the phenotype.

I'll thank a lot any suggestion.

-- 
*J. Luis Santomé Collazo*
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Re: [galaxy-user] Warning message

[Daniel Blankenberg]

Hi Rolando,

You'll need to remove the old blast datatypes from your datatypes_conf.xml 
file. If you haven't added any new datatypes manually yourself, you can copy 
the datatypes_conf.xml.sample file over of your datatypes_conf.xml file.

Also, in the future questions about local Galaxy instances should be sent to 
the galaxy-dev mailing list. 


Thanks for using Galaxy,

Dan


On Nov 12, 2012, at 10:31 PM, Rolando Mantilla wrote:

 I'm having issues with the FASTQ_Groomer. What I have done it first I 
 downloaded an SRA file created by an Ion torrent sequencer from the NCBI 
 site. Then used the fastq-dump app from the NCBI site to covert the .sra file 
 to .fastq file. When I uploaded the data into galaxy it recognized it as a 
 fastq(as it should) but when I try to run the FASTQ groomer I get the message 
 and warnings below. I also have already downloaded the the blast_datatypes 
 tool from the tool_shed. I truly don't know what the issue is, any help
 An error occurred running this job: Groomed 12376 sanger reads into sanger 
 reads.
   
 WARNING:galaxy.datatypes.registry:Error loading datatype with extension 
 'blastxml': 'module' object has no attribute 'BlastXml'  
 WARNING:galaxy.datatypes.registry:Overriding conflicting datatype with 
 extension 'blastxml', using datatype from /mnt/galaxyData/tmp/tmpdP_cZ7.
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 Galaxy analysis and other features on the public server
 at usegalaxy.org.  Please keep all replies on the list by
 using reply all in your mail client.  For discussion of
 local Galaxy instances and the Galaxy source code, please
 use the Galaxy Development list:
 
  http://lists.bx.psu.edu/listinfo/galaxy-dev
 
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 please use the interface at:
 
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at usegalaxy.org.  Please keep all replies on the list by
using reply all in your mail client.  For discussion of
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