How to add "rdata" datatype into galaxy ?

[inestiouiri]

I'm trying to run FROGSSTAT Phyloseq Import Data but i always get WARNING:galaxy.model:Datatype class not found for extension 'rdata' Thanks

[mariabernard]

which version of Galaxy are you using ?

[inestiouiri]

16

[mariabernard]

Hello

Sorry, for the delay. I commonly use galaxy 16.10 where the rdata datatype is included in the datatypes_conf.xml

You should manually add it or upgrade galaxy (I will try to add a comment in the Readme)

[inestiouiri]

Could you please paste the datatype line for rdata from you datatypes_conf.xml here for me. Thanks

[mariabernard]

in /conf/datatypes_conf.xml

<datatype extension="RData" type="galaxy.datatypes.binary:RData" display_in_upload="true" description="Stored data from an R session"/>

and in /lib/galaxy/datatypes/binary.py (I hope you have a Binary class)

class RData( Binary ):
    """Generic R Data file datatype implementation"""
    file_ext = 'RData'

    def sniff( self, filename ):
        rdata_header = b'RDX2\nX\n'
        try:
            header = open(filename, 'rb').read(7)
            if header == rdata_header:
                return True

            header = gzip.open( filename ).read(7)
            if header == rdata_header:
                return True
        except:
            return False

Binary.register_sniffable_binary_format('RData', 'RData', RData)

but it's maybe only usefull for sniffable datatype. There is maybe a simpler way to declare new datatype in the config file whithout changing source code.

[inestiouiri]

@mariabernard Thank you for your help. I've tried this but still get the same error knowing that i've just edited datatypes_conf.xml because i don't have a binary class. error is below:

subprocess.CalledProcessError: Command 'Rscript -e "rmarkdown::render('/usr/local/galaxy/tools/FROGS_2/app/r_import_data.Rmd',output_file='/scratch/database/files/025/dataset_25871.dat', params=list(biomfile='/scratch/database/files/024/dataset_24154.dat', samplefile='/scratch/database/files/025/dataset_25808.dat', treefile='/scratch/database/files/025/dataset_25795.dat', normalization=TRUE, outputRdata='/scratch/database/files/025/dataset_25870.dat', ranks=''), intermediates_dir='/scratch/database/files/025')" 2> /dev/null' returned non-zero exit status 139

WARNING:galaxy.model:Datatype class not found for extension 'rdata'

[mariabernard]

Hi

I am sorry but I am not an expert of Galaxy and this is not a FROGS problem. The only advice I can give is to upgrade you galaxy version.

I juste check when this datatype was added (which is not simple as multiple release were done at the same date, and release ordre is not always consistent). Release 15.07 has the rdata datatype, but not release 15.03.

So I think that your galaxy version is much older than you think.

Best regards