Workflows with run time parameters broken?
Hi all, I noticed a new problem with our local Galaxy (recently updated), but found it happens on the public installation too. I can edit workflows, and create run time parameters like ${Name} or ${Name with spaces}, but when I come to run the workflow I get an error:
Server Error An error occurred. See the error logs for more information. (Turn debug on to display exception reports here)
e.g. This trivial example takes a FASTA file, does a minimum length filter, and tries to rename the output to a run time parameter string: http://main.g2.bx.psu.edu/u/peterjc/w/test-workflow-filter-fasta-min-length-... Is this a known issue? I couldn't find a match on the bitbucket tracker. Thanks, Peter
The issue you're seeing is actually related to improper initialization of the workflow parameters index in the special case where a particular parameter is only used in a rename action and not in a tool step. This is fixed in revision 5400:6cacf178a129. -Dannon On Apr 20, 2011, at 10:28 AM, Peter Cock wrote:
Hi all,
I noticed a new problem with our local Galaxy (recently updated), but found it happens on the public installation too.
I can edit workflows, and create run time parameters like ${Name} or ${Name with spaces}, but when I come to run the workflow I get an error:
Server Error An error occurred. See the error logs for more information. (Turn debug on to display exception reports here)
e.g. This trivial example takes a FASTA file, does a minimum length filter, and tries to rename the output to a run time parameter string:
http://main.g2.bx.psu.edu/u/peterjc/w/test-workflow-filter-fasta-min-length-...
Is this a known issue? I couldn't find a match on the bitbucket tracker.
Thanks,
Peter ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Hi Dan, On Wed, Apr 20, 2011 at 3:47 PM, Dannon Baker <dannonbaker@me.com> wrote:
The issue you're seeing is actually related to improper initialization of the workflow parameters index in the special case where a particular parameter is only used in a rename action and not in a tool step. This is fixed in revision 5400:6cacf178a129.
So it should already fixed on galaxy-central (and the test server), but hasn't yet been pushed to galaxy-dist (and the live server). As we run our local sever from galaxy-dist (as recommended), I'll be patient and try to avoid this. Also I'll try to recreate my more complicated workflow (which in addition to doing dataset renames, was also trying to use workflow parameters in the final tool's arguments) under galaxy-central to confirm the fix. Thanks, Peter
Hi, I've followed this thread with interest. I have had a problem on one of my workflows, it fails to perform a sort on a dataset returning the error "sort: invalid number at field start: invalid count at start of `None,Nonen'". However, this error makes no sense. When I ask it to run the job again with the input it is supposed to sort it works just fine. When the workflow is getting ready to be submitted I've checked and double checked all the links and they are correct too. Is my error related in some way? Does this make sense? Best Wishes, David. __________________________________ Dr David A. Matthews Senior Lecturer in Virology Room E49 Department of Cellular and Molecular Medicine, School of Medical Sciences University Walk, University of Bristol Bristol. BS8 1TD U.K. Tel. +44 117 3312058 Fax. +44 117 3312091 D.A.Matthews@bristol.ac.uk On 20 Apr 2011, at 15:47, Dannon Baker wrote:
The issue you're seeing is actually related to improper initialization of the workflow parameters index in the special case where a particular parameter is only used in a rename action and not in a tool step. This is fixed in revision 5400:6cacf178a129.
-Dannon
On Apr 20, 2011, at 10:28 AM, Peter Cock wrote:
Hi all,
I noticed a new problem with our local Galaxy (recently updated), but found it happens on the public installation too.
I can edit workflows, and create run time parameters like ${Name} or ${Name with spaces}, but when I come to run the workflow I get an error:
Server Error An error occurred. See the error logs for more information. (Turn debug on to display exception reports here)
e.g. This trivial example takes a FASTA file, does a minimum length filter, and tries to rename the output to a run time parameter string:
http://main.g2.bx.psu.edu/u/peterjc/w/test-workflow-filter-fasta-min-length-...
Is this a known issue? I couldn't find a match on the bitbucket tracker.
Thanks,
Peter ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
I'll take a look at the workflow in question, if you'd like to share it with me at this email address, 'dannonbaker@me.com'. -Dannon On Apr 20, 2011, at 12:42 PM, David Matthews wrote:
Hi,
I've followed this thread with interest. I have had a problem on one of my workflows, it fails to perform a sort on a dataset returning the error "sort: invalid number at field start: invalid count at start of `None,Nonen'". However, this error makes no sense. When I ask it to run the job again with the input it is supposed to sort it works just fine. When the workflow is getting ready to be submitted I've checked and double checked all the links and they are correct too. Is my error related in some way? Does this make sense?
Best Wishes, David.
__________________________________ Dr David A. Matthews
Senior Lecturer in Virology Room E49 Department of Cellular and Molecular Medicine, School of Medical Sciences University Walk, University of Bristol Bristol. BS8 1TD U.K.
Tel. +44 117 3312058 Fax. +44 117 3312091
D.A.Matthews@bristol.ac.uk
On 20 Apr 2011, at 15:47, Dannon Baker wrote:
The issue you're seeing is actually related to improper initialization of the workflow parameters index in the special case where a particular parameter is only used in a rename action and not in a tool step. This is fixed in revision 5400:6cacf178a129.
-Dannon
On Apr 20, 2011, at 10:28 AM, Peter Cock wrote:
Hi all,
I noticed a new problem with our local Galaxy (recently updated), but found it happens on the public installation too.
I can edit workflows, and create run time parameters like ${Name} or ${Name with spaces}, but when I come to run the workflow I get an error:
Server Error An error occurred. See the error logs for more information. (Turn debug on to display exception reports here)
e.g. This trivial example takes a FASTA file, does a minimum length filter, and tries to rename the output to a run time parameter string:
http://main.g2.bx.psu.edu/u/peterjc/w/test-workflow-filter-fasta-min-length-...
Is this a known issue? I couldn't find a match on the bitbucket tracker.
Thanks,
Peter ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Done, many thanks... Best Wishes, David. __________________________________ Dr David A. Matthews Senior Lecturer in Virology Room E49 Department of Cellular and Molecular Medicine, School of Medical Sciences University Walk, University of Bristol Bristol. BS8 1TD U.K. Tel. +44 117 3312058 Fax. +44 117 3312091 D.A.Matthews@bristol.ac.uk On 20 Apr 2011, at 17:44, Dannon Baker wrote:
I'll take a look at the workflow in question, if you'd like to share it with me at this email address, 'dannonbaker@me.com'.
-Dannon
On Apr 20, 2011, at 12:42 PM, David Matthews wrote:
Hi,
I've followed this thread with interest. I have had a problem on one of my workflows, it fails to perform a sort on a dataset returning the error "sort: invalid number at field start: invalid count at start of `None,Nonen'". However, this error makes no sense. When I ask it to run the job again with the input it is supposed to sort it works just fine. When the workflow is getting ready to be submitted I've checked and double checked all the links and they are correct too. Is my error related in some way? Does this make sense?
Best Wishes, David.
__________________________________ Dr David A. Matthews
Senior Lecturer in Virology Room E49 Department of Cellular and Molecular Medicine, School of Medical Sciences University Walk, University of Bristol Bristol. BS8 1TD U.K.
Tel. +44 117 3312058 Fax. +44 117 3312091
D.A.Matthews@bristol.ac.uk
On 20 Apr 2011, at 15:47, Dannon Baker wrote:
The issue you're seeing is actually related to improper initialization of the workflow parameters index in the special case where a particular parameter is only used in a rename action and not in a tool step. This is fixed in revision 5400:6cacf178a129.
-Dannon
On Apr 20, 2011, at 10:28 AM, Peter Cock wrote:
Hi all,
I noticed a new problem with our local Galaxy (recently updated), but found it happens on the public installation too.
I can edit workflows, and create run time parameters like ${Name} or ${Name with spaces}, but when I come to run the workflow I get an error:
Server Error An error occurred. See the error logs for more information. (Turn debug on to display exception reports here)
e.g. This trivial example takes a FASTA file, does a minimum length filter, and tries to rename the output to a run time parameter string:
http://main.g2.bx.psu.edu/u/peterjc/w/test-workflow-filter-fasta-min-length-...
Is this a known issue? I couldn't find a match on the bitbucket tracker.
Thanks,
Peter ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
It doesn't look like you're using workflow parameters in this workflow. Or were you trying to, and something perhaps went wrong? As to your "None" error, in the sort in step 21 of the workflow you shared it looks like the column selection is None, and I'm guessing that's the problem here. Let me know if entering a valid column there doesn't resolve this and I can investigate. -Dannon On Apr 20, 2011, at 12:47 PM, David Matthews wrote:
Done, many thanks...
Best Wishes, David.
__________________________________ Dr David A. Matthews
Senior Lecturer in Virology Room E49 Department of Cellular and Molecular Medicine, School of Medical Sciences University Walk, University of Bristol Bristol. BS8 1TD U.K.
Tel. +44 117 3312058 Fax. +44 117 3312091
D.A.Matthews@bristol.ac.uk
On 20 Apr 2011, at 17:44, Dannon Baker wrote:
I'll take a look at the workflow in question, if you'd like to share it with me at this email address, 'dannonbaker@me.com'.
-Dannon
On Apr 20, 2011, at 12:42 PM, David Matthews wrote:
Hi,
I've followed this thread with interest. I have had a problem on one of my workflows, it fails to perform a sort on a dataset returning the error "sort: invalid number at field start: invalid count at start of `None,Nonen'". However, this error makes no sense. When I ask it to run the job again with the input it is supposed to sort it works just fine. When the workflow is getting ready to be submitted I've checked and double checked all the links and they are correct too. Is my error related in some way? Does this make sense?
Best Wishes, David.
__________________________________ Dr David A. Matthews
Senior Lecturer in Virology Room E49 Department of Cellular and Molecular Medicine, School of Medical Sciences University Walk, University of Bristol Bristol. BS8 1TD U.K.
Tel. +44 117 3312058 Fax. +44 117 3312091
D.A.Matthews@bristol.ac.uk
On 20 Apr 2011, at 15:47, Dannon Baker wrote:
The issue you're seeing is actually related to improper initialization of the workflow parameters index in the special case where a particular parameter is only used in a rename action and not in a tool step. This is fixed in revision 5400:6cacf178a129.
-Dannon
On Apr 20, 2011, at 10:28 AM, Peter Cock wrote:
Hi all,
I noticed a new problem with our local Galaxy (recently updated), but found it happens on the public installation too.
I can edit workflows, and create run time parameters like ${Name} or ${Name with spaces}, but when I come to run the workflow I get an error:
Server Error An error occurred. See the error logs for more information. (Turn debug on to display exception reports here)
e.g. This trivial example takes a FASTA file, does a minimum length filter, and tries to rename the output to a run time parameter string:
http://main.g2.bx.psu.edu/u/peterjc/w/test-workflow-filter-fasta-min-length-...
Is this a known issue? I couldn't find a match on the bitbucket tracker.
Thanks,
Peter ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Hello all. I am re-exploring Galaxy after a year hiatus. While I searched the archives to no avail it is possible that my question/complaint was already answered. If so, please ignore. I find the placement of Mouse-ear Cress (arabidopsis) in the 'select a reference genome' list to be strange. It appears that the list is sorted by scientific name first and then by name. However this does not seem to be true in the case of arabidopsis thaliana but is true for arabidopsis lyrata. Granted the auto-complete feature (e.g., when I start typing 'ara...' then the selection list is narrowed) helps in finding A. thaliana however, especially for an organism beginning with 'a' the misplacement of A. thaliana (in my opinion) is striking. On a side note, I find the drop down for the reference genome to be too small (in terms of width in particular). I have to view and scroll through a lot of two or three line entries but if the width was larger then it would be possible to see more entries at one time. -- Rick Westerman westerman@purdue.edu Bioinformatics specialist at the Genomics Facility. Phone: (765) 494-0505 FAX: (765) 496-7255 Department of Horticulture and Landscape Architecture 625 Agriculture Mall Drive West Lafayette, IN 47907-2010 Physically located in room S049, WSLR building
Hello Rick, Welcome back :) Thanks for the suggestions! Making it easier for users to locate data is important. I'll pass these on to our genome database guru (Kelly) for consideration. Best wishes and let us know if you need help or have other observations/suggestions. All feedback is appreciated, Thanks! Jen Galaxy team On 4/20/11 1:16 PM, Rick Westerman wrote:
Hello all. I am re-exploring Galaxy after a year hiatus. While I searched the archives to no avail it is possible that my question/complaint was already answered. If so, please ignore.
I find the placement of Mouse-ear Cress (arabidopsis) in the 'select a reference genome' list to be strange. It appears that the list is sorted by scientific name first and then by name. However this does not seem to be true in the case of arabidopsis thaliana but is true for arabidopsis lyrata. Granted the auto-complete feature (e.g., when I start typing 'ara...' then the selection list is narrowed) helps in finding A. thaliana however, especially for an organism beginning with 'a' the misplacement of A. thaliana (in my opinion) is striking.
On a side note, I find the drop down for the reference genome to be too small (in terms of width in particular). I have to view and scroll through a lot of two or three line entries but if the width was larger then it would be possible to see more entries at one time.
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org
participants (5)
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Dannon Baker -
David Matthews -
Jennifer Jackson -
Peter Cock -
Rick Westerman