Worklist failing on collection with AttributeError: 'object' object has no attribute 'collection'

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Worklist failing on collection with AttributeError: 'object' object has no attribute 'collection'

BigTA78

Hello all


I am trying to invoke a workflow on a paired dataset collection (simple trim step (trimmomatic) followed by align (RNAStar)) through the GUI.

Each time I run, I get the prompt:

 

Successfully invoked workflow RNASeq v1.0.

You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered

 

suggesting that all is well, but nothing gets added to my history. I am not sending data to another history, but to the current one.

 

If I look into the logs, I see the error AttributeError: 'object' object has no attribute 'collection' as the reason for failing

 

If I modify the workflow to work on individual datasets, it runs successfully. It seems to be purely when I run on collections.

 

This is my own Galaxy instance (17.05), not the public server.


Any help appreciated

 

Tony (Galaxy Newbie)


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Re: Worklist failing on collection with AttributeError: 'object' object has no attribute 'collection'

Marius van den Beek
Hi Tony,

could you include the traceback that leads up to this error ?
That should help us narrow down the cause.

Best,
Marius

On 3 October 2017 at 18:37, Brooks, Tony <[hidden email]> wrote:

Hello all


I am trying to invoke a workflow on a paired dataset collection (simple trim step (trimmomatic) followed by align (RNAStar)) through the GUI.

Each time I run, I get the prompt:

 

Successfully invoked workflow RNASeq v1.0.

You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered

 

suggesting that all is well, but nothing gets added to my history. I am not sending data to another history, but to the current one.

 

If I look into the logs, I see the error AttributeError: 'object' object has no attribute 'collection' as the reason for failing

 

If I modify the workflow to work on individual datasets, it runs successfully. It seems to be purely when I run on collections.

 

This is my own Galaxy instance (17.05), not the public server.


Any help appreciated

 

Tony (Galaxy Newbie)


___________________________________________________________
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/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/


___________________________________________________________
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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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Re: Worklist failing on collection with AttributeError: 'object' object has no attribute 'collection'

Marius van den Beek
Hi Tony,

I was able to reproduce the problem, there is indeed a problem.
We're working on fixing this, but you should be able to include a separate input step
before starting your workflow (In the left panel, under inputs -> Input dataset collection).
Make sure to set the Collection type of this input step to "Paired", and hopefully your workflow should run successfully.

Let me know if that works for you,
Marius

On 4 October 2017 at 15:02, Marius van den Beek <[hidden email]> wrote:
Hi Tony,

could you include the traceback that leads up to this error ?
That should help us narrow down the cause.

Best,
Marius

On 3 October 2017 at 18:37, Brooks, Tony <[hidden email]> wrote:

Hello all


I am trying to invoke a workflow on a paired dataset collection (simple trim step (trimmomatic) followed by align (RNAStar)) through the GUI.

Each time I run, I get the prompt:

 

Successfully invoked workflow RNASeq v1.0.

You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered

 

suggesting that all is well, but nothing gets added to my history. I am not sending data to another history, but to the current one.

 

If I look into the logs, I see the error AttributeError: 'object' object has no attribute 'collection' as the reason for failing

 

If I modify the workflow to work on individual datasets, it runs successfully. It seems to be purely when I run on collections.

 

This is my own Galaxy instance (17.05), not the public server.


Any help appreciated

 

Tony (Galaxy Newbie)


___________________________________________________________
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/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/



___________________________________________________________
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/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/