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Test circos 0.69.8+galaxy7 #26

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jennaj opened this issue Mar 10, 2022 · 5 comments
Closed

Test circos 0.69.8+galaxy7 #26

jennaj opened this issue Mar 10, 2022 · 5 comments

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@jennaj
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jennaj commented Mar 10, 2022

This tool is pending an update at org galaxyproject/usegalaxy-playbook#346

org is at 0.69.8+galaxy7 (known issues, but don't impact GTN tutorials, curious how tests turn out)
.eu is still at 0.69.8+galaxy9
mts is at 0.69.8+galaxy10

tool_id=toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy7
@jennaj
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jennaj commented Mar 10, 2022

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy7

@mvdbeek
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mvdbeek commented Mar 10, 2022

Results (powered by Planemo)

Summary

State Count
Total 2
Passed 0
Error 0
Failure 2
Skipped 0
Failed s
  • ❌ toolshed.g2.bx.psu.edu/repos/iuc/circos/circos (Test tool test #1)

    Problems:

    • Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy7, exit_code: 21, stderr: Use of uninitialized value in subroutine entry at /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-3cf5c7d734898be0f8d76d0fbf3face5f99ca4b3a9b294235f9271dd27115368/bin/../lib/Circos/Configuration.pm line 781.
Can't call method "colorExact" on an undefined value at /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-3cf5c7d734898be0f8d76d0fbf3face5f99ca4b3a9b294235f9271dd27115368/bin/../lib/Circos/Colors.pm line 348, <F> line 2.
.

    • Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy7, exit_code: 21, stderr: Use of uninitialized value in subroutine entry at /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-3cf5c7d734898be0f8d76d0fbf3face5f99ca4b3a9b294235f9271dd27115368/bin/../lib/Circos/Configuration.pm line 781.
Can't call method "colorExact" on an undefined value at /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-3cf5c7d734898be0f8d76d0fbf3face5f99ca4b3a9b294235f9271dd27115368/bin/../lib/Circos/Colors.pm line 348, <F> line 2.
.

    • Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy7, exit_code: 21, stderr: Use of uninitialized value in subroutine entry at /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-3cf5c7d734898be0f8d76d0fbf3face5f99ca4b3a9b294235f9271dd27115368/bin/../lib/Circos/Configuration.pm line 781.
Can't call method "colorExact" on an undefined value at /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-3cf5c7d734898be0f8d76d0fbf3face5f99ca4b3a9b294235f9271dd27115368/bin/../lib/Circos/Colors.pm line 348, <F> line 2.
.

    Command Line:

    • 

      • 

    

    Exit Code:
    

      

    • 

      21
      

      • 

    

    Standard Error:
    

      

    • 

      Use of uninitialized value in subroutine entry at /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-3cf5c7d734898be0f8d76d0fbf3face5f99ca4b3a9b294235f9271dd27115368/bin/../lib/Circos/Configuration.pm line 781.
Can't call method "colorExact" on an undefined value at /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-3cf5c7d734898be0f8d76d0fbf3face5f99ca4b3a9b294235f9271dd27115368/bin/../lib/Circos/Colors.pm line 348, <F> line 2.

      

      • 

    

    Standard Output:
    

      

    • 

      debuggroup summary 0.26s welcome to circos v0.69-8 15 Jun 2019 on Perl 5.026002
debuggroup summary 0.26s current working directory /corral4/main/jobs/041/306/41306838/working
debuggroup summary 0.26s command /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-3cf5c7d734898be0f8d76d0fbf3face5f99ca4b3a9b294235f9271dd27115368/bin/circos -conf circos/conf/circos.conf -noparanoid
debuggroup summary 0.26s loading configuration from file circos/conf/circos.conf
debuggroup summary 0.26s found conf file circos/conf/circos.conf
debuggroup summary 2.39s debug will appear for these features: output,summary
debuggroup summary 2.40s bitmap output image ./circos.png
debuggroup summary 2.40s SVG output image ./circos.svg
debuggroup summary 2.40s parsing karyotype and organizing ideograms
debuggroup summary 2.41s karyotype has 2 chromosomes of total size 56,082
debuggroup summary 2.41s applying global and local scaling
debuggroup summary 2.41s allocating image, colors and brushes

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
reference_genome
{"ref": {"__current_case__": 2, "genome_fasta": {"values": [{"id": 94315153, "src": "hda"}]}, "ref_source": "history"}}

      

      
ideogram
{"angle_offset": "-90", "angle_orientation": "clockwise", "bands": {"band_stroke_color": "#000000", "band_stroke_thickness": "0", "band_transparency": "3", "fill_bands": "true", "show_bands": "true"}, "chromosomes_reverse": null, "ideogram_labels": {"parallel": "true", "radius_offset": "0.075", "show_label": "true", "size": "24"}, "limit_chromosomes": null, "pairwise_spacing": [], "radius": "0.9", "spacing": "0.5", "thickness": "30.0", "units": "mb"}

      

      
plot_options
{"background": {"__current_case__": 1, "background_color": "#ffffff", "background_select": "color"}, "colour_profile": null, "radius": "1500"}

      

      
sec_tdd
{"data": []}

      

      
sec_links
{"data": []}

      

      
scaling
{"zooms": []}

      

      
ticks
{"radius": "1.0", "skip_first_label": "false", "skip_last_label": "false", "tick_group": []}

      

      
limits
{"max_ideograms": "200", "max_links": "25000", "max_points_per_track": "25000", "max_ticks": "5000"}

      

      
outputs
{"png": "true", "svg": "true", "tar": "false"}

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"auto"

      
      

      

      • 

    

    

    • 

  • 

    ❌ toolshed.g2.bx.psu.edu/repos/iuc/circos/circos (Test test against test.galaxyproject.org #2)
    

    Problems:
    

      

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy7, exit_code: 21, stderr: Use of uninitialized value in subroutine entry at /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-3cf5c7d734898be0f8d76d0fbf3face5f99ca4b3a9b294235f9271dd27115368/bin/../lib/Circos/Configuration.pm line 781.
Can't call method "colorExact" on an undefined value at /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-3cf5c7d734898be0f8d76d0fbf3face5f99ca4b3a9b294235f9271dd27115368/bin/../lib/Circos/Colors.pm line 348, <F> line 2.
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy7, exit_code: 21, stderr: Use of uninitialized value in subroutine entry at /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-3cf5c7d734898be0f8d76d0fbf3face5f99ca4b3a9b294235f9271dd27115368/bin/../lib/Circos/Configuration.pm line 781.
Can't call method "colorExact" on an undefined value at /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-3cf5c7d734898be0f8d76d0fbf3face5f99ca4b3a9b294235f9271dd27115368/bin/../lib/Circos/Colors.pm line 348, <F> line 2.
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy7, exit_code: 21, stderr: Use of uninitialized value in subroutine entry at /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-3cf5c7d734898be0f8d76d0fbf3face5f99ca4b3a9b294235f9271dd27115368/bin/../lib/Circos/Configuration.pm line 781.
Can't call method "colorExact" on an undefined value at /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-3cf5c7d734898be0f8d76d0fbf3face5f99ca4b3a9b294235f9271dd27115368/bin/../lib/Circos/Colors.pm line 348, <F> line 2.
.

      

      • 

    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      21
      

      • 

    

    Standard Error:
    

      

    • 

      Use of uninitialized value in subroutine entry at /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-3cf5c7d734898be0f8d76d0fbf3face5f99ca4b3a9b294235f9271dd27115368/bin/../lib/Circos/Configuration.pm line 781.
Can't call method "colorExact" on an undefined value at /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-3cf5c7d734898be0f8d76d0fbf3face5f99ca4b3a9b294235f9271dd27115368/bin/../lib/Circos/Colors.pm line 348, <F> line 2.

      

      • 

    

    Standard Output:
    

      

    • 

      debuggroup summary 0.21s welcome to circos v0.69-8 15 Jun 2019 on Perl 5.026002
debuggroup summary 0.22s current working directory /corral4/main/jobs/041/306/41306844/working
debuggroup summary 0.22s command /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-3cf5c7d734898be0f8d76d0fbf3face5f99ca4b3a9b294235f9271dd27115368/bin/circos -conf circos/conf/circos.conf -noparanoid
debuggroup summary 0.22s loading configuration from file circos/conf/circos.conf
debuggroup summary 0.22s found conf file circos/conf/circos.conf
debuggroup summary 0.63s debug will appear for these features: output,summary
debuggroup summary 0.63s bitmap output image ./circos.png
debuggroup summary 0.63s SVG output image ./circos.svg
debuggroup summary 0.64s parsing karyotype and organizing ideograms
debuggroup summary 0.65s karyotype has 2 chromosomes of total size 56,082
debuggroup summary 0.65s applying global and local scaling
debuggroup summary 0.65s allocating image, colors and brushes

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
reference_genome
{"ref": {"__current_case__": 2, "genome_fasta": {"values": [{"id": 94315153, "src": "hda"}]}, "ref_source": "history"}}

      

      
ideogram
{"angle_offset": "-90", "angle_orientation": "clockwise", "bands": {"band_stroke_color": "#000000", "band_stroke_thickness": "0", "band_transparency": "3", "fill_bands": "true", "show_bands": "true"}, "chromosomes_reverse": null, "ideogram_labels": {"parallel": "true", "radius_offset": "0.075", "show_label": "true", "size": "24"}, "limit_chromosomes": null, "pairwise_spacing": [], "radius": "0.9", "spacing": "0.5", "thickness": "30.0", "units": "kb"}

      

      
plot_options
{"background": {"__current_case__": 1, "background_color": "#ffffff", "background_select": "color"}, "colour_profile": null, "radius": "1500"}

      

      
sec_tdd
{"data": [{"__index__": 0, "minmax": {"__current_case__": 1, "minmax_select": "no"}, "minsize": "0.0", "orientation": "false", "plot_format": {"__current_case__": 0, "data_source": {"values": [{"id": 94315166, "src": "hda"}]}, "format_specific": {"extend_bins": "false", "fill_color": "#ffdcfc", "fill_color_alpha": "1.0", "fill_under": "true", "stroke_color": "#000000", "stroke_color_alpha": "1.0", "stroke_thickness": "1"}, "plot_format_select": "histogram"}, "r0": "0.8", "r1": "0.9", "sec_axes": {"axes": [], "only_if_data": "always"}, "sec_bkgs": {"backgrounds": [], "only_if_data": "always"}, "sec_rule": {"rules": []}, "zdepth": "0"}, {"__index__": 1, "minmax": {"__current_case__": 1, "minmax_select": "no"}, "minsize": "0.0", "orientation": "false", "plot_format": {"__current_case__": 5, "data_source": {"values": [{"id": 94315166, "src": "hda"}]}, "format_specific": {"fill_color": "#555555", "fill_color_alpha": "1.0", "glyph": "circle", "glyph_size": "8", "stroke_color": "#000000", "stroke_color_alpha": "1.0", "stroke_thickness": "1"}, "plot_format_select": "scatter"}, "r0": "0.7", "r1": "0.8", "sec_axes": {"axes": [], "only_if_data": "always"}, "sec_bkgs": {"backgrounds": [], "only_if_data": "always"}, "sec_rule": {"rules": []}, "zdepth": "0"}, {"__index__": 2, "minmax": {"__current_case__": 1, "minmax_select": "no"}, "minsize": "0.0", "orientation": "false", "plot_format": {"__current_case__": 6, "data_source": {"values": [{"id": 94315168, "src": "hda"}]}, "format_specific": {"fill_color": "#000000", "fill_color_alpha": "1.0", "layers": "15", "margin": "0.002", "overflow": {"__current_case__": 0, "overflow_behavior": "hide"}, "padding": "8.0", "stroke_color": "#000000", "stroke_color_alpha": "1.0", "stroke_thickness": "1", "thickness": "15.0"}, "plot_format_select": "tile"}, "r0": "0.6", "r1": "0.7", "sec_axes": {"axes": [], "only_if_data": "always"}, "sec_bkgs": {"backgrounds": [], "only_if_data": "always"}, "sec_rule": {"rules": []}, "zdepth": "0"}]}

      

      
sec_links
{"data": [{"__index__": 0, "advanced": {"bezier_radius_purity": "0.75", "crest": "0.5", "perturbation": {"__current_case__": 1, "perturb": "no"}}, "bezier_radius": "0.1", "color": "#000000", "color_alpha": "1.0", "data_source": {"values": [{"id": 94315169, "src": "hda"}]}, "linktype": {"__current_case__": 0, "pattern": "solid", "ribbon": "yes", "twist": ""}, "minsize": "0.0", "radius": "0.59", "sec_link_rule": {"rules": []}, "thickness": "15.0", "zdepth": "0"}]}

      

      
scaling
{"zooms": []}

      

      
ticks
{"radius": "1.0", "skip_first_label": "false", "skip_last_label": "false", "tick_group": [{"__index__": 0, "color": "#000000", "size": "10.0", "spacing": "1.0", "ticks": {"__current_case__": 1, "show_tick_labels": "no"}}, {"__index__": 1, "color": "#000000", "size": "10.0", "spacing": "5.0", "ticks": {"__current_case__": 0, "format": "%.1f", "format_ext": "true", "label_offset": "10.0", "label_size": "20.0", "show_tick_labels": "yes"}}]}

      

      
limits
{"max_ideograms": "200", "max_links": "25000", "max_points_per_track": "25000", "max_ticks": "5000"}

      

      
outputs
{"png": "true", "svg": "true", "tar": "false"}

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"fasta"

      
      

      

      • 

    

    

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  @jennaj





  


    

      

  

    

        
    
    

  


      
          
  
      
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            jennaj
  

      

      

      commented


        Mar 10, 2022


      
    


  





      


        


  
    

      
          
That the known karyotype issue. We should update, I'll ping in lab

      		
    

  





        


            

            

              
            

        

      


      

            
  

    
  
    
    

  

  



    












      

  
          

  

    
  


  

      

    @jennaj
jennaj



    mentioned this issue
    
      Mar 10, 2022
    





  


  

      
  
  Closed

  







  









      

  
      



  

  @jennaj





  


    

      

  

    

        
    
    

  


      
          
  
      
            Copy link

  

      
    

  


  

      

  
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  Author


  


  

    

      

      
            jennaj
  

      

      

      commented


        Mar 15, 2022


      
    


  





      


        


  
    

      
          
/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy10

      		
    

  





        


            

            

              
            

        

      


      

            
  

    
  
    
    

  

  



    












      

  
      



  

  @mvdbeek





  


    

      

  

    

        
    
    

  


      
          
  
      
            Copy link

  

      
    

  


  

      

  
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            mvdbeek
  

      

      

      commented


        Mar 15, 2022


      
    


  





      


        


  
    

      
          
Results (powered by Planemo)


Summary



  

  

  

  

  

  








State
Count






Total
3




Passed
1




Error
2




Failure
0




Skipped
0






Errored s

    

  • 

    ❌ toolshed.g2.bx.psu.edu/repos/iuc/circos/circos (Test test against test.galaxyproject.org #2)
    

    Execution Problem:
    

      

    • 

      Value ('1') must fulfill float('200') <= value <= float('inf'), Value ('1') must fulfill float('200') <= value <= float('inf'), Value ('1') must fulfill float('200') <= value <= float('inf'), Value ('1') must fulfill float('200') <= value <= float('inf')

      

      • 

    

    

    • 

  • 

    ❌ toolshed.g2.bx.psu.edu/repos/iuc/circos/circos (Test Test Prokka 1.14.6+galaxy1 #3)
    

    Execution Problem:
    

      

    • 

      Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .

      

      • 

    

    

    • 





Passed s

    

  • 

    ✅ toolshed.g2.bx.psu.edu/repos/iuc/circos/circos (Test tool test #1)
    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      0
      

      • 

    

    Standard Error:
    

      

    • 

      Use of uninitialized value in subroutine entry at /usr/local/bin/../lib/Circos/Configuration.pm line 781.

      

      • 

    

    Standard Output:
    

      

    • 

      debuggroup summary 0.24s welcome to circos v0.69-8 15 Jun 2019 on Perl 5.026002
debuggroup summary 0.24s current working directory /corral4/main/jobs/041/396/41396294/working
debuggroup summary 0.24s command /usr/local/bin/circos -conf circos/conf/circos.conf -noparanoid
debuggroup summary 0.24s loading configuration from file circos/conf/circos.conf
debuggroup summary 0.24s found conf file circos/conf/circos.conf
debuggroup summary 0.47s debug will appear for these features: output,summary
debuggroup summary 0.47s bitmap output image ./circos.png
debuggroup summary 0.47s SVG output image ./circos.svg
debuggroup summary 0.48s parsing karyotype and organizing ideograms
debuggroup summary 0.51s karyotype has 2 chromosomes of total size 56,082
debuggroup summary 0.51s applying global and local scaling
debuggroup summary 0.51s allocating image, colors and brushes
debuggroup summary 9.89s drawing 2 ideograms of total size 56,082
debuggroup summary 9.89s drawing highlights and ideograms
debuggroup output 9.90s generating output
debuggroup output 10.38s created PNG image ./circos.png (40 kb)
debuggroup output 10.38s created SVG image ./circos.svg (2 kb)

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
reference_genome
{"ref": {"__current_case__": 2, "genome_fasta": {"values": [{"id": 94474101, "src": "hda"}]}, "ref_source": "history"}}

      

      
ideogram
{"angle_offset": "-90", "angle_orientation": "clockwise", "bands": {"band_stroke_color": "#000000", "band_stroke_thickness": "0", "band_transparency": "3", "fill_bands": "true", "show_bands": "true"}, "chromosomes_reverse": null, "ideogram_labels": {"parallel": "true", "radius_offset": "0.075", "show_label": "true", "size": "24"}, "limit_chromosomes": null, "pairwise_spacing": [], "radius": "0.9", "spacing": "0.5", "thickness": "30.0", "units": "mb"}

      

      
plot_options
{"background": {"__current_case__": 1, "background_color": "#ffffff", "background_select": "color"}, "colour_profile": null, "radius": "1500"}

      

      
sec_tdd
{"data": []}

      

      
sec_links
{"data": []}

      

      
scaling
{"zooms": []}

      

      
ticks
{"radius": "1.0", "skip_first_label": "false", "skip_last_label": "false", "tick_group": []}

      

      
limits
{"max_ideograms": "200", "max_links": "25000", "max_points_per_track": "25000", "max_ticks": "5000"}

      

      
outputs
{"png": "true", "svg": "true", "tar": "false"}

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"auto"

      
      

      

      • 

    

    

    • 




      		
    

  





        


            

            

              
            

        

      


      

            
  

    
  
    
    

  

  



    












      

  
            

    

      
    

    


      

          @jennaj
jennaj




            closed this as completed


      Mar 16, 2022

    

  


    


  

  

    
  


  

      

    @mvdbeek
mvdbeek



    mentioned this issue
    
      Nov 10, 2022
    





  


  

      
  
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      2 participants
    

    

        
          @mvdbeek 
        
          @jennaj