Workflow 'Input Dataset' Ressolution Issue
Hello Galaxy Dev, Consider the workflow found in 'Strelka_Workflow_Sequential' image Here it is in a different view 'Strelka_Sequential_Workflow_Different_View' Notice That the first input dataset links to the fetch_interval tool and the first preprocess tool. And the second input dataset links only to the second preprocess tool. When you run the workflow, what actually happens is the first input dataset goes to the fetch_interval tools and the second input dataset goes to both preprocessing tools. (Look at final two images). They have essentially executed the same tool twice. Where it should be an execution with a normal file and an execution with a tumour file. Why is this happening? What can I do to fix this? Thanks, Marco Albuquerque
This sounds like it corresponds to this issue https://github.com/galaxyproject/galaxy/issues/776. Is it possible that upgrading Galaxy to the latest 15.07 fixes the issue? On Thu, Oct 8, 2015 at 7:40 PM, Marco Albuquerque <marcoalbuquerque.sfu@gmail.com> wrote:
Hello Galaxy Dev,
Consider the workflow found in 'Strelka_Workflow_Sequential' image
Here it is in a different view 'Strelka_Sequential_Workflow_Different_View'
Notice That the first input dataset links to the fetch_interval tool and the first preprocess tool. And the second input dataset links only to the second preprocess tool.
When you run the workflow, what actually happens is the first input dataset goes to the fetch_interval tools and the second input dataset goes to both preprocessing tools. (Look at final two images). They have essentially executed the same tool twice. Where it should be an execution with a normal file and an execution with a tumour file.
Why is this happening? What can I do to fix this?
Thanks,
Marco Albuquerque
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Well, my Cloudman galaxy instance is installing 15.07 revision 990501d2d9. Is there maybe a different revision I should be using? Marco On Sun, Oct 11, 2015 at 11:03 AM, John Chilton <jmchilton@gmail.com> wrote:
This sounds like it corresponds to this issue https://github.com/galaxyproject/galaxy/issues/776. Is it possible that upgrading Galaxy to the latest 15.07 fixes the issue?
Hello Galaxy Dev,
Consider the workflow found in 'Strelka_Workflow_Sequential' image
Here it is in a different view 'Strelka_Sequential_Workflow_Different_View'
Notice That the first input dataset links to the fetch_interval tool and
On Thu, Oct 8, 2015 at 7:40 PM, Marco Albuquerque <marcoalbuquerque.sfu@gmail.com> wrote: the
first preprocess tool. And the second input dataset links only to the second preprocess tool.
When you run the workflow, what actually happens is the first input dataset goes to the fetch_interval tools and the second input dataset goes to both preprocessing tools. (Look at final two images). They have essentially executed the same tool twice. Where it should be an execution with a normal file and an execution with a tumour file.
Why is this happening? What can I do to fix this?
Thanks,
Marco Albuquerque
___________________________________________________________ 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/mailinglists/
Yeah - release_15.07 is a moving target that bug fixes get added to. 990501d2d9 doesn't seem to have this fix yet. On Sun, Oct 11, 2015 at 5:09 PM, Marco Albuquerque <marcoalbuquerque.sfu@gmail.com> wrote:
Well, my Cloudman galaxy instance is installing 15.07 revision 990501d2d9.
Is there maybe a different revision I should be using?
Marco
On Sun, Oct 11, 2015 at 11:03 AM, John Chilton <jmchilton@gmail.com> wrote:
This sounds like it corresponds to this issue https://github.com/galaxyproject/galaxy/issues/776. Is it possible that upgrading Galaxy to the latest 15.07 fixes the issue?
On Thu, Oct 8, 2015 at 7:40 PM, Marco Albuquerque <marcoalbuquerque.sfu@gmail.com> wrote:
Hello Galaxy Dev,
Consider the workflow found in 'Strelka_Workflow_Sequential' image
Here it is in a different view 'Strelka_Sequential_Workflow_Different_View'
Notice That the first input dataset links to the fetch_interval tool and the first preprocess tool. And the second input dataset links only to the second preprocess tool.
When you run the workflow, what actually happens is the first input dataset goes to the fetch_interval tools and the second input dataset goes to both preprocessing tools. (Look at final two images). They have essentially executed the same tool twice. Where it should be an execution with a normal file and an execution with a tumour file.
Why is this happening? What can I do to fix this?
Thanks,
Marco Albuquerque
___________________________________________________________ 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/mailinglists/
So in other words, there is no release that I can update my cloudman instance to? Marco On Sun, Oct 11, 2015 at 3:49 PM, John Chilton <jmchilton@gmail.com> wrote:
Yeah - release_15.07 is a moving target that bug fixes get added to. 990501d2d9 doesn't seem to have this fix yet.
On Sun, Oct 11, 2015 at 5:09 PM, Marco Albuquerque <marcoalbuquerque.sfu@gmail.com> wrote:
Well, my Cloudman galaxy instance is installing 15.07 revision 990501d2d9.
Is there maybe a different revision I should be using?
Marco
On Sun, Oct 11, 2015 at 11:03 AM, John Chilton <jmchilton@gmail.com> wrote:
This sounds like it corresponds to this issue https://github.com/galaxyproject/galaxy/issues/776. Is it possible that upgrading Galaxy to the latest 15.07 fixes the issue?
On Thu, Oct 8, 2015 at 7:40 PM, Marco Albuquerque <marcoalbuquerque.sfu@gmail.com> wrote:
Hello Galaxy Dev,
Consider the workflow found in 'Strelka_Workflow_Sequential' image
Here it is in a different view 'Strelka_Sequential_Workflow_Different_View'
Notice That the first input dataset links to the fetch_interval tool
and
the first preprocess tool. And the second input dataset links only to the second preprocess tool.
When you run the workflow, what actually happens is the first input dataset goes to the fetch_interval tools and the second input dataset goes to both preprocessing tools. (Look at final two images). They have essentially executed the same tool twice. Where it should be an execution with a normal file and an execution with a tumour file.
Why is this happening? What can I do to fix this?
Thanks,
Marco Albuquerque
___________________________________________________________ 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/mailinglists/
No if you update to the latest release_15.07 it should be fixed. I don't know if CloudMan has an easy way to do that, but you can do it from the command-line with something like the following commands: % git fetch --all % git checkout release_15.07 -John On Mon, Oct 12, 2015 at 4:09 AM, Marco Albuquerque <marcoalbuquerque.sfu@gmail.com> wrote:
So in other words, there is no release that I can update my cloudman instance to?
Marco
On Sun, Oct 11, 2015 at 3:49 PM, John Chilton <jmchilton@gmail.com> wrote:
Yeah - release_15.07 is a moving target that bug fixes get added to. 990501d2d9 doesn't seem to have this fix yet.
On Sun, Oct 11, 2015 at 5:09 PM, Marco Albuquerque <marcoalbuquerque.sfu@gmail.com> wrote:
Well, my Cloudman galaxy instance is installing 15.07 revision 990501d2d9.
Is there maybe a different revision I should be using?
Marco
On Sun, Oct 11, 2015 at 11:03 AM, John Chilton <jmchilton@gmail.com> wrote:
This sounds like it corresponds to this issue https://github.com/galaxyproject/galaxy/issues/776. Is it possible that upgrading Galaxy to the latest 15.07 fixes the issue?
On Thu, Oct 8, 2015 at 7:40 PM, Marco Albuquerque <marcoalbuquerque.sfu@gmail.com> wrote:
Hello Galaxy Dev,
Consider the workflow found in 'Strelka_Workflow_Sequential' image
Here it is in a different view 'Strelka_Sequential_Workflow_Different_View'
Notice That the first input dataset links to the fetch_interval tool and the first preprocess tool. And the second input dataset links only to the second preprocess tool.
When you run the workflow, what actually happens is the first input dataset goes to the fetch_interval tools and the second input dataset goes to both preprocessing tools. (Look at final two images). They have essentially executed the same tool twice. Where it should be an execution with a normal file and an execution with a tumour file.
Why is this happening? What can I do to fix this?
Thanks,
Marco Albuquerque
___________________________________________________________ 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/mailinglists/
participants (2)
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John Chilton -
Marco Albuquerque