Accessing local installation of biomart results in "Unexpected format to the list of available marts"
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6 months ago
anhvo711 • 0

I have downloaded and launched the webserver for a local installation of Biomart 0.9 using these directions. After using MartConfigurator to download a mart, I am attempting to access the webserver using

listMarts(host = "IP.address", port = 9000, path = "/martservice/marts")

This results in the R error:

"Error: Unexpected format to the list of available marts. Please check the following URL manually, and try ?listMarts for advice."

When visiting the URL, I get this warning and a page that is supposed to start with "MartRegistry", but does not.

This XML file does not appear to have any style information associated with it. The document tree is shown below.

<marts>
<mart mart="gene_ensembl" config="gene_ensembl_config" group="" isHidden="false" meta="" operation="SINGLESELECT" description="gene_ensembl_config" displayName="ensembl_mart_ensembl" name="gene_ensembl_config"/>
<mart mart="gene_ensembl" config="gene_ensembl_config_1" group="" isHidden="false" meta="" operation="SINGLESELECT" description="gene_ensembl_config_1" displayName="gene_ensembl_config_1" name="gene_ensembl_config_1"/>
</marts>


Any idea on what I am doing wrong & how to fix this issue?

rna-seq biomart mart martconfigurator xml • 355 views
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This XML file does not appear to have any style information associated with it. The document tree is shown below.

this message is unrelated to your problem. It's just an aesthetic information.

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Any idea what the problem actually is? Why are the marts not of correct format?

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Sounds like you did not actually manage to download a mart. Did you do the stuff on page 7 and 8 of the guide?

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Yes, I did all of that and downloaded from ensembl since biomart.org was not giving any marts

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You may want to write to Ensembl help desk about this. If they provide a solution please come back and post it here.

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6 months ago
Mike Smith ★ 1.7k

Cross posted the Bioconductor Support Site, with an answer here