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 ___________________________________________________________ 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/
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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