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 /* Davide Cittaro Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy tel.: +39(02)574303007 e-mail: davide.cittaro@ifom-ieo-campus.it */
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.
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 /* Davide Cittaro Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy tel.: +39(02)574303007 e-mail: davide.cittaro@ifom-ieo-campus.it */
participants (2)
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Davide Cittaro -
Jeremy Goecks