Hello Lubos,

this should be fixed with https://github.com/galaxyproject/galaxy/pull/1897.
If you pull in the latest changes (git pull) on the release_16.01 branch
things should work again.

Cheers,
Marius

On 15 March 2016 at 18:54, Lubos Klucar <klu...@embnet.sk> wrote:

> Hi,
>
> after upgrading from 15.10 to 16.01, the trackster visualisation tool is
> partly defective. It can successfully show e.g. GFF tracks, but after
> adding e.g. BAM track nothing is shown. The only suspicious debug output I
> could get when loading non-working-track is:
>
> galaxy.webapps.galaxy.api.datasets ERROR 2016-03-15 11:44:38,853 Error in
> dataset API at listing contents: Expected bytes, got unicode: Expected
> bytes, got unicode
> Traceback (most recent call last):
>   File "/usr/local/galaxy-prod/lib/galaxy/webapps/galaxy/api/datasets.py",
> line 66, in show
>     rval = self._data( trans, dataset, **kwd )
>   File "/usr/local/galaxy-prod/lib/galaxy/webapps/galaxy/api/datasets.py",
> line 235, in _data
>     ref_seq=region, mean_depth=mean_depth, **kwargs )
>   File
> "/usr/local/galaxy-prod/lib/galaxy/visualization/data_providers/genome.py",
> line 192, in get_data
>     iterator = self.get_iterator( data_file, chrom, start, end, **kwargs )
>   File
> "/usr/local/galaxy-prod/lib/galaxy/visualization/data_providers/genome.py",
> line 892, in get_iterator
>     data = data_file.fetch( start=start, end=end, reference=chrom )
>   File "pysam/calignmentfile.pyx", line 868, in
> pysam.calignmentfile.AlignmentFile.fetch (pysam/calignmentfile.c:10170)
>   File "pysam/calignmentfile.pyx", line 787, in
> pysam.calignmentfile.AlignmentFile.parse_region
> (pysam/calignmentfile.c:9605)
>   File "pysam/calignmentfile.pyx", line 1576, in
> pysam.calignmentfile.AlignmentFile.gettid (pysam/calignmentfile.c:16665)
>   File "pysam/calignmentfile.pyx", line 640, in
> pysam.calignmentfile.AlignmentFile.get_tid (pysam/calignmentfile.c:8208)
>   File "pysam/cutils.pyx", line 106, in pysam.cutils.force_bytes
> (pysam/cutils.c:2170)
> TypeError: Expected bytes, got unicode
>
> Any help to solve this problem would be highly appreciated!
>
> many thanks
> --
>
>                 Lubos Klucar
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