Hi Anthonius,

Do you have the BEDTools installed and its directory added to your PATH environment variable? Trackster uses compressed file formats to reduce the amount of data transfers.

I hope this helps,

Sam

On Wed, Aug 21, 2013 at 4:11 PM, Anthonius deBoer <thondeboer@me.com> wrote:

Hi,

I am using the latest version of galaxy at my local installation and I try to use trackster to display a simple BED file, but it invariably complains about not having a converter for this datatype and it tells me to check my datatypes_conf.xml which I did (not sure what I should be looking for, but this is the section on BED files...

Am I missing a converter? And why would a BED file even needed to be converted?

Thanks

Thon

    <datatype extension="bed" type="galaxy.datatypes.interval:Bed" display_in_upload="true">

      <converter file="bed_to_gff_converter.xml" target_datatype="gff"/>

      <converter file="interval_to_coverage.xml" target_datatype="coverage"/>

      <converter file="bed_to_bgzip_converter.xml" target_datatype="bgzip"/>

      <converter file="bed_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/>

      <converter file="bed_to_summary_tree_converter.xml" target_datatype="summary_tree"/>

      <converter file="bed_to_fli_converter.xml" target_datatype="fli"/>

      <!-- <display file="ucsc/interval_as_bed.xml" /> -->

      <!-- <display file="genetrack.xml" /> -->

      <display file="igb/bed.xml" />

    </datatype>

    <datatype extension="bedgraph" type="galaxy.datatypes.interval:BedGraph" display_in_upload="true">

      <converter file="bedgraph_to_bigwig_converter.xml" target_datatype="bigwig"/>

    </datatype>

    <datatype extension="bedstrict" type="galaxy.datatypes.interval:BedStrict" />

    <!-- <datatype extension="bed6" type="galaxy.datatypes.interval:Bed6">

      <converter file="bed_to_genetrack_converter.xml" target_datatype="genetrack"/>

    </datatype> -->

    <datatype extension="bed12" type="galaxy.datatypes.interval:Bed12" />

    <datatype extension="len" type="galaxy.datatypes.chrominfo:ChromInfo" display_in_upload="true">

      <converter file="len_to_linecount.xml" target_datatype="linecount" />

    </datatype>

    <datatype extension="bigbed" type="galaxy.datatypes.binary:BigBed" mimetype="application/octet-stream" dis

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