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/

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(a)embnet.sk <mailto: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 ___________________________________________________________ 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/