Workflows With Run Time Parameters Broken?

Question: Workflows With Run Time Parameters Broken?

7.6 years ago by

Peter Cock • 1.4k

European Union

Peter Cock • 1.4k 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: 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-10 Is this a known issue? I couldn't find a match on the bitbucket tracker. Thanks, Peter

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modified 7.6 years ago • written 7.6 years ago by Peter Cock • 1.4k

7.6 years ago by

Dannon Baker ♦ 3.7k

United States

Dannon Baker ♦ 3.7k 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

ADD COMMENT • link written 7.6 years ago by Dannon Baker ♦ 3.7k

Hi Dan, 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

ADD REPLY • link written 7.6 years ago by Peter Cock • 1.4k

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

ADD REPLY • link written 7.6 years ago by David Matthews • 630

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

ADD REPLY • link written 7.6 years ago by Dannon Baker ♦ 3.7k

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

ADD REPLY • link written 7.6 years ago by Rick Westerman • 30

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 -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org

ADD REPLY • link written 7.6 years ago by Jennifer Hillman Jackson ♦ 25k

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

ADD REPLY • link written 7.6 years ago by David Matthews • 630

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

ADD REPLY • link written 7.6 years ago by Dannon Baker ♦ 3.7k

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