vcf support

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vcf support

Davide Cittaro
Hi all, I've just pulled last dev brief update

hg pull -u -r 8729d2e29b02

I can see vcf support in several galaxy files (datatypes/tabular.py, datatypes/converters/vcf_to_summary_tree_converter.py, visualization/tracks/data_providers.py...) but it is not visible in the main web interface (i.e. I can't assign VCF as type and it is not automatically recognized).... what can I check to make this properly work?

d

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Re: vcf support

Jeremy Goecks
> I can see vcf support in several galaxy files (datatypes/tabular.py, datatypes/converters/vcf_to_summary_tree_converter.py, visualization/tracks/data_providers.py...) but it is not visible in the main web interface (i.e. I can't assign VCF as type and it is not automatically recognized).... what can I check to make this properly work?

You need to update your datatypes_conf.xml file to include support for VCF:

(1) In the <datatypes> section, add the following:

        <datatype extension="vcf" type="galaxy.datatypes.tabular:Vcf" display_in_upload="true">
            <converter file="vcf_to_interval_index_converter.xml" target_datatype="interval_index"/>
            <converter file="vcf_to_summary_tree_converter.xml" target_datatype="summary_tree"/>    
        </datatype>

(2) In the <sniffers> section, add the following:

        <sniffer type="galaxy.datatypes.tabular:Vcf"/>


Thanks,
J.
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Re: vcf support

Davide Cittaro

On Nov 29, 2010, at 5:02 PM, Jeremy Goecks wrote:

I can see vcf support in several galaxy files (datatypes/tabular.py, datatypes/converters/vcf_to_summary_tree_converter.py, visualization/tracks/data_providers.py...) but it is not visible in the main web interface (i.e. I can't assign VCF as type and it is not automatically recognized).... what can I check to make this properly work?

You need to update your datatypes_conf.xml file to include support for VCF:


Right, right! Thanks!

d
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Davide Cittaro

Cogentech - Consortium for Genomic Technologies
via adamello, 16
20139 Milano
Italy

tel.: +39(02)574303007
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