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 <klu...@embnet.sk
<mailto: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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--

                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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