Hi Thon

double check your datatypes_conf.xml (which was not touched/changed during the update process, since it is listed in the .hgignore file, I guess) with the new datatypes_conf.xml.sample file for any changes regarding converters for "bed" files



Regards, Hans-Rudolf


On 08/22/2013 02:51 AM, Anthonius deBoer wrote:
Yep...

$ bedtools --version
bedtools v2.17.0

Thon

On Aug 21, 2013, at 01:40 PM, sam guerler <aysam.guer...@gmail.com> wrote:

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 <thondeb...@me.com
<mailto:thondeb...@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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