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

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/