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 <[email protected]> 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 <[email protected]
<mailto:[email protected]>> 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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