I should have mentioned that is of course possible to export() the track to
BED, WIG, GFF, etc, and upload it as a custom track manually. This allows,
for example, uploading to a user account, so that the session/tracks can be
shared with others.

Michael

On Wed, Jan 11, 2012 at 8:53 AM, Michael Lawrence <michafla@gene.com> wrote:

> The bug below is caused by the attempt to upload a GRanges, instead of a
> RangedData. This is basically on its way to being fixed in devel.
>
> That said, it won't work anyway, because some time in the last 6 months or
> so UCSC must have changed its (totally undocumented, internal) interface
> for uploading tracks, and I have not had the time or desire to reverse
> engineer it yet again. We could probably ask UCSC for help on this, but
> this feature is not of use to me nor my employer, so I just can't commit
> the time to it. Unless someone steps up to help, I'll probably have to
> disable it.
>
> Sorry,
> Michael
>
>
> On Wed, Jan 11, 2012 at 4:35 AM, simon [guest] <guest@bioconductor.org>wrote:
>
>>
>> I could not load a custom track to the UCSC genome browser, so I tried it
>> according to the rtracklayer vignette and I got also an error. What am I
>> doing wrong?
>>
>> thanks!
>> simon
>>
>>  -- output of sessionInfo():
>>
>> > data(targets)
>> > targetRanges <- IRanges(targets$start, targets$end)
>> > targetTrack <- with(targets,GRangesForUCSCGenome("hg18", chrom,
>> targetRanges, strand,name, target))
>> > session <- browserSession("UCSC")
>> > track(session, "targets") <- targetTrack
>> Fehler in genome(seqinfo(x)) :
>>  Fehler bei der Auswertung des Argumentes 'x' bei der Methodenauswahl
>> für Funktion 'genome': Fehler in .normargSeqlengths(seqlengths,
>> seqnames) :
>>  supplied 'seqlengths' must be a vector
>>
>>
>> R version 2.14.0 (2011-10-31)
>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>
>> locale:
>>  [1] LC_CTYPE=de_AT.UTF-8          LC_NUMERIC=C
>>  [3] LC_TIME=de_AT.UTF-8           LC_COLLATE=de_AT.UTF-8
>>  [5] LC_MONETARY=de_AT.UTF-8       LC_MESSAGES=de_AT.UTF-8
>>  [7] LC_PAPER=de_AT.UTF-8          LC_NAME=de_AT.UTF-8
>>  [9] LC_ADDRESS=de_AT.UTF-8        LC_TELEPHONE=de_AT.UTF-8
>> [11] LC_MEASUREMENT=de_AT.UTF-8    LC_IDENTIFICATION=de_AT.UTF-8
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>> [1] GenomicRanges_1.6.4 IRanges_1.12.5      rtracklayer_1.14.4
>> [4] RCurl_1.8-0         bitops_1.0-4.1      rj_1.0.2-5
>>
>> loaded via a namespace (and not attached):
>> [1] Biostrings_2.22.0 BSgenome_1.22.0   rj.gd_1.0.2-2     tools_2.14.0
>> [5] XML_3.6-2         zlibbioc_1.0.0
>>
>>
>> --
>> Sent via the guest posting facility at bioconductor.org.
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor@r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>
>

	[[alternative HTML version deleted]]

