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.