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> 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/ >
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