Great, thanks, all is working now!

all the best

Lubos

On 15. 3. 2016 19:48, Marius van den Beek wrote:
Hi Lubos,

I opened a Pull Request on
https://github.com/galaxyproject/galaxy/pull/1930, which should
hopefully fix the problem.
If you want to give it a try, you can do
`git fetch origin pull/1930/head:more_bytestring_for_pysam`
and
`git checkout more_bytestring_for_pysam`.
When the problem has been solved, you can switch back to release_16.01
by doing `git checkout release_16.01`.

Thanks for reporting the error,
Marius


On 15 March 2016 at 19:25, Marius van den Beek <m.vandenb...@gmail.com
<mailto:m.vandenb...@gmail.com>> wrote:

    Yes, `git checkout release_16.01` should do it, but wait a second,
    there might actually be a problem,
    since ` File
    "/usr/local/galaxy-prod/lib/galaxy/visualization/data_providers/genome.py",
    line 892, in get_iterator`,
    while the PR addresses 354-356!


    On 15 March 2016 at 19:23, Lubos Klucar <klu...@embnet.sk
    <mailto:klu...@embnet.sk>> wrote:



        On 15. 3. 2016 19:15, Marius van den Beek wrote:

            Hi Lubos,

            hmm, I'm surprised about this.
            Just to make sure, you are on the release_16.01 branch?
            (`git branch` should highlight release_16.01)
            This PR hasn't been merged into dev yet.


        Hi Marius,

        it seems I need more help with git, not the Galaxy!. ;-) My git
        branch gives me:

           dev
        * master

        How should I 'switch' to 16.01??..

        regards

        Lubos

            Cheers,
            Marius

            On 15 March 2016 at 19:08, Lubos Klucar <klu...@embnet.sk
            <mailto:klu...@embnet.sk>
            <mailto:klu...@embnet.sk <mailto:klu...@embnet.sk>>> wrote:

                 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>
                     <mailto:klu...@embnet.sk <mailto:klu...@embnet.sk>>
                     <mailto:klu...@embnet.sk <mailto:klu...@embnet.sk>
            <mailto: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
            <tel:%2B421%202%205930%207413> <tel:%2B421%202%205930%207413>
                                  Fax.: +421 2 5930 7416
            <tel:%2B421%202%205930%207416> <tel:%2B421%202%205930%207416>



        --

                         Lubos Klucar

                         Institute of Molecular Biology
                         Slovak Academy of Science
                         Dubravska cesta 21
                         845 51  Bratislava 45
                         Slovakia

                         Tel.: +421 2 5930 7413
        <tel:%2B421%202%205930%207413>
                         Fax.: +421 2 5930 7416
        <tel:%2B421%202%205930%207416>




--

                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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