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.guerler@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 <thondeboer@me.com <mailto: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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