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 <klucar@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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