Dear Marius,
thanks for help, but it looks our galaxy is up to date:
remote: Counting objects: 111, done.
remote: Compressing objects: 100% (23/23), done.
remote: Total 111 (delta 82), reused 75 (delta 75), pack-reused 13
Receiving objects: 100% (111/111), 39.85 KiB, done.
Resolving deltas: 100% (82/82), completed with 29 local objects.
From https://github.com/galaxyproject/galaxy
8423fe7..23c3300 dev -> origin/dev
5a50a46..65a5b08 release_16.01 -> origin/release_16.01
Already up-to-date.
After Galaxy restart the problem still persist...
all the best
Lubos
On 15. 3. 2016 18:59, Marius van den Beek 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 <[email protected]
<mailto:[email protected]>> 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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--
Lubos Klucar
Institute of Molecular Biology
Slovak Academy of Science
Dubravska cesta 21
845 51 Bratislava 45
Slovakia
Tel.: +421 2 5930 7413
Fax.: +421 2 5930 7416
___________________________________________________________
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