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.vandenbeek(a)gmail.com
<mailto: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(a)embnet.sk
<mailto: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(a)embnet.sk
<mailto:klucar@embnet.sk>
<mailto: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(a)embnet.sk <mailto:klucar@embnet.sk>
<mailto:klucar@embnet.sk <mailto:klucar@embnet.sk>>
<mailto: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> <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