New subject: Trackster in 16.01 broken

15 Mar 2016

      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.vandenbeek@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 <klucar@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 <klucar@embnet.sk
<mailto:klucar@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 <klucar@embnet.sk
        <mailto:klucar@embnet.sk>
        <mailto:klucar@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
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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>
                     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

Re: [galaxy-dev] Trackster in 16.01 broken

Marius van den Beek

Lubos Klucar

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