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 18:59, Marius van den Beek <m.vandenb...@gmail.com> wrote: > 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 >> ___________________________________________________________ >> 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: >> https://lists.galaxyproject.org/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ > > >
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