Re: [galaxy-dev] Removing job in error state

[Ryan G]

Thanks.   That fixed it.

On Thu, Aug 4, 2016 at 3:19 AM, Hans-Rudolf Hotz  wrote:

> Hi Ryan
>
> If the "Stop Jobs" option on the Admin page does not work, you can go for
> the direct way by manually interacting with the PostgreSQL database:
>
> Change the state to "error"  in the 'job' table, eg:
>
> update job set state='error' where id=12772;
>
>
> As always, be very careful when you directly access the PostgreSQL
> database! Make sure your database is properly backed up. And you should
> only consider this as the very last option.
>
>
> Hans-Rudolf
>
>
> On 08/04/2016 06:02 AM, Ryan G wrote:
>
>> Hi - In the Manage Jobs admin job, I have a job from a user that never
>> ran successfully.   It shows:
>> Job ID  UserLast Update ToolState   Inputs  Command Line
>> Job Runner
>> PID/Cluster ID
>> 12772   u...@company.com   654
>> hours ago
>> cshl_fastx_collapsernew 13653 error NoneNoneNone
>>
>>
>> How do I remove this job?  I can't find a way to delete it.
>>
>>
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[galaxy-dev] Retrieving bam index file for visualization outside of Galaxy

[Ouellette, Scott]

Hi all,

I have a use case where I need to programmatically download both the .bam and 
it's index file to run IGV outside of Galaxy, but have not found a 
straightforward way to do so.
It seems that Galaxy always generates this .bai file under the hood, and I can 
download it manually by clicking the "save" icon on the dataset in my history. 
Although, the application I am coding for relies on the bioblend Python library.

---

In bioblend I see a field returned upon a 
`DatasetClient().show_dataset()` but that is as 
far as I've got:

"meta_files": [
{
"file_type": "bam_index"
}
],

Any help is appreciated!

Thanks,
Scott O.

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Re: [galaxy-dev] Removing job in error state

[Hans-Rudolf Hotz]

Hi Ryan

If the "Stop Jobs" option on the Admin page does not work, you can go 
for the direct way by manually interacting with the PostgreSQL database:


Change the state to "error"  in the 'job' table, eg:

update job set state='error' where id=12772;


As always, be very careful when you directly access the PostgreSQL 
database! Make sure your database is properly backed up. And you should 
only consider this as the very last option.



Hans-Rudolf


On 08/04/2016 06:02 AM, Ryan G wrote:

Hi - In the Manage Jobs admin job, I have a job from a user that never
ran successfully.   It shows:
Job ID  UserLast Update ToolState   Inputs  Command LineJob 
Runner
PID/Cluster ID
12772   u...@company.com 654 hours ago
cshl_fastx_collapsernew 13653 error NoneNoneNone


How do I remove this job?  I can't find a way to delete it.


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