Bug with workflow

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Bug with workflow

juliech
Hi all,
I've a bug with the use of workflow. I've created my own workflow and
since the latest update the workflow can be launched correctly but not
completely!!!

The first steps works with outputs on history, a job runs in
job_working_directory for each of these steps. But for my final step :
no job begin in job_working_directory so no data in history because
the jobs don't exist.

In my workflow the outputs are selected to be not hidden and the final
step is connected with other steps.

Any other one have this problem ?

Thanks.

Julie
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Re: Bug with workflow

John Chilton-4
There is likely a failed job somewhere in your history? Can you look
at that for details - standard out, standard error, etc...?

Can you open the workflow in the workflow editor and see if it still
looks the same as before the update?

Also, can you export the workflow and send it to me?

Thanks,
-John

On Thu, Jul 3, 2014 at 2:20 AM, julie dubois <[hidden email]> wrote:

> Hi all,
> I've a bug with the use of workflow. I've created my own workflow and
> since the latest update the workflow can be launched correctly but not
> completely!!!
>
> The first steps works with outputs on history, a job runs in
> job_working_directory for each of these steps. But for my final step :
> no job begin in job_working_directory so no data in history because
> the jobs don't exist.
>
> In my workflow the outputs are selected to be not hidden and the final
> step is connected with other steps.
>
> Any other one have this problem ?
>
> Thanks.
>
> Julie
> ___________________________________________________________
> 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:
>   http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
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Re: Bug with workflow

juliech
Hi,
Thanks for your answer.
I've no failed job in my history.
I've checked the workflow and it is the same as before update.
But your answer highlight another point ! The tool I use in my final
step has been modified after update of galaxy and not tested alone.
When I've tested this tool alone, I've seen this error in the middle
panel "output" not found (it was a variable name which have been
changed after update !!!).

It's the first time that I have such error with no entry in history
preventing a check of stderr and stdout, so I didn't think that it can
be come from my tool.

Thanks for your help.

Julie

2014-07-07 2:22 GMT+02:00 John Chilton <[hidden email]>:

> There is likely a failed job somewhere in your history? Can you look
> at that for details - standard out, standard error, etc...?
>
> Can you open the workflow in the workflow editor and see if it still
> looks the same as before the update?
>
> Also, can you export the workflow and send it to me?
>
> Thanks,
> -John
>
> On Thu, Jul 3, 2014 at 2:20 AM, julie dubois <[hidden email]> wrote:
>> Hi all,
>> I've a bug with the use of workflow. I've created my own workflow and
>> since the latest update the workflow can be launched correctly but not
>> completely!!!
>>
>> The first steps works with outputs on history, a job runs in
>> job_working_directory for each of these steps. But for my final step :
>> no job begin in job_working_directory so no data in history because
>> the jobs don't exist.
>>
>> In my workflow the outputs are selected to be not hidden and the final
>> step is connected with other steps.
>>
>> Any other one have this problem ?
>>
>> Thanks.
>>
>> Julie
>> ___________________________________________________________
>> 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:
>>   http://lists.bx.psu.edu/
>>
>> To search Galaxy mailing lists use the unified search at:
>>   http://galaxyproject.org/search/mailinglists/
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Delete an account (Galaxy local instance)

Pat-74100
In reply to this post by John Chilton-4
Dear Galaxy developers.

Is it possible to delete an account (user not active anymore) on a Galaxy local instance as Admin ?

Regards,
Pat

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Re: Delete an account (Galaxy local instance)

Pat-74100
I've found it:

I've modified it in the file universe_wgsi.ini and now I can delete user by the admin tool panel.
The problem is: when I delete the account and purge it why it still remain in the list ? is it possible to delete it completely ??


From: [hidden email]
To: [hidden email]
Date: Mon, 7 Jul 2014 09:49:48 +0000
Subject: [galaxy-dev] Delete an account (Galaxy local instance)

Dear Galaxy developers.

Is it possible to delete an account (user not active anymore) on a Galaxy local instance as Admin ?

Regards,
Pat

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Re: Delete an account (Galaxy local instance)

Nate Coraor (nate@bx.psu.edu)
On Jul 7, 2014, at 6:11 AM, Pat-74100 <[hidden email]> wrote:

I've found it:

I've modified it in the file universe_wgsi.ini and now I can delete user by the admin tool panel. 
The problem is: when I delete the account and purge it why it still remain in the list ? is it possible to delete it completely ??

Hi Pat,

Because Galaxy needs to track data provenance, we do not ever actually remove metadata such as this from the database.

--nate



From: [hidden email]
To: [hidden email]
Date: Mon, 7 Jul 2014 09:49:48 +0000
Subject: [galaxy-dev] Delete an account (Galaxy local instance)

Dear Galaxy developers.

Is it possible to delete an account (user not active anymore) on a Galaxy local instance as Admin ?

Regards,
Pat

___________________________________________________________ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
___________________________________________________________
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and other Galaxy lists, please use the interface at:
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___________________________________________________________
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