> On May 23, 2016, at 3:34 PM, Carl Eberhard wrote:
>
> There's a way to get the current history data through a non-api url:
> /history/current_history_json
That works, but to get the current history for a user I need to set the
galaxysession cookie. So it is not
Hi Sarah,
Did you activate the "allow_user_dataset_purge" function on the galaxy.ini ?
allow_user_dataset_purge = True
Cheers,
Yvan
- Mail original -
> De: "Sarah Maman"
> À: galaxy-dev@lists.galaxyproject.org
> Envoyé: Lundi 23 Mai 2016 18:57:22
>
Hi Ryan,
I have seen the same strange behavior with some tabular files. My findings were
to display these tabular datasets through the scratchbook Just a
"bidouille" ;) Maybe this will work for you too
Cheers,
Yvan
- Mail original -
> De: "Ryan G"
On Tue, May 24, 2016 at 11:42 AM, Raymond Wan wrote:
> Hi Peter,
>
>
> On Tue, May 24, 2016 at 6:29 PM, Peter Cock wrote:
>> In case you didn't know, Galaxy likes to keep all BAM files in
>> coordinate sorted order with a BAI index (using
Hi Peter,
On Tue, May 24, 2016 at 6:29 PM, Peter Cock wrote:
> In case you didn't know, Galaxy likes to keep all BAM files in
> coordinate sorted order with a BAI index (using samtools).
> Somehow this is failing on your system (perhaps a suitable
> version of
Hello Ray
Just to clarify, for us it wasn't dependent on the tool - it was
actually the version of samtools installed in the 'galaxy' user's
environment i.e. on the 'galaxy' user's PATH.
I set it explicitly by creating a file called "local_env.sh" in the
'config' directory of the Galaxy
Dear all,
We are experiencing a crash of our Galaxy instance (latest git log is
early January 2016) and it seems unable to restart. The last entries
in paster.log says the following:
galaxy.web.framework.base DEBUG 2016-05-24 17:46:42,593 Enabling
'histories' API controller, class:
Hello Ray
One of my colleagues encountered a similar-sounding error on our local
test instance, where an unsorted BAM file seemed to crash the Galaxy
handler processes and prevented them from restarting.
In our case the default samtools version in the Galaxy environment was
0.1.18; we found
To follow up on what Peter says
It is the code in
https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/datatypes/binary.py
from line 182
class Bam( Binary ):
This code (set_meta) is called after the tool has finished running while it is
copying the resulting data into the galaxy
Hello
Since yesterday I've the following warning at Galaxy () start-up :
Retrying (Retry(total=4, connect=None, read=None, redirect=None)) after
connection broken by
'ConnectTimeoutError(object at 0x3149390>, 'Connection to wheels.galaxyproject.org timed out.
(connect timeout=15)')':
Hi Fernandez,
We saw something very like that with mixed versions of Linux,
specifically our Galaxy head node where pysam was installed
had CentOS 7, but the node where Galaxy was trying to run
the metadata detection was CentOS 6. Unfortunately I do
not have a record of the exact traceback - but
Hello guys,
I’m still stuck on this error.
I’ve installed a brand new galaxy v16.01
And when I start it, I get the big error mentioned below.
Here’s the last message in the error:
ImportError:
/home/galaxy/galaxy-v16.01/.venv/lib/python2.7/site-packages/pysam/libchtslib.so:
undefined symbol:
Hello Peter,
What would your suggestion be?
Wait until a new version of galaxy is compatible with my Oracle Linux 6 ?
Best regards,
Edgar Fernandez
System Administrator (Linux)
Direction Générale des Technologies de l'Information et de la Communication
Université de Montréal
PAVILLON
most_recently_used *was* broken - thanks for finding that. A pull request
going back to the 16.01 release is here:
https://github.com/galaxyproject/galaxy/pull/2407
A planning issue for a session API is here:
https://github.com/galaxyproject/galaxy/issues/2404
On Tue, May 24, 2016 at 4:16 PM,
Ok - if it's not zebra striped and it's word wrapping, then it's somehow
not displaying as tabular - you're correct.
If you click on the 'View details' button of that dataset (the 'i' with the
circle around it shown when the dataset is expanded in the right hand side
of the 'Analyze Data' page),
Hi Edgar,
Are your Galaxy server AND your cluster are all running
Oracle Linux 6?
If yes, my guess about the cluster using an older version
of Linux compared to the Galaxy server is unrelated.
Peter
On Tue, May 24, 2016 at 7:47 PM, Fernandez Edgar
wrote:
> Hello
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