problem with running microscopy pipeline

[tomkal]

Before submitting an issue, please be sure to

• Read the contributing instructions
• Update to the latest version (run git pull; sudo -H pip3 install .)

This issue affects

• Centrality estimation (gpseqc_estimate)
• Ranks comparison (gpseqc_compare)

What did you do (e.g., steps to reproduce)

bicro@orion:~/Desktop/user_folders/Tomek/microscopy_pipeline/IMR90_iTK225-240_080618$ gpseq_anim -d dapi -s cy5 -t 36 --note "TK GPSeq YFISH asynch IMR90 deconvolved, center as percentile" --center-as-percentile -r '/home/bicro/Desktop/user_folders/Tomek/microscopy_pipeline/IMR90_iTK226-241_080618/Data_input_iTK226_233' '/home/bicro/Desktop/user_folders/Tomek/microscopy_pipeline/IMR90_iTK226-241_080618/Data_output_iTK226_233'  --sigma-smooth 0.05 -n
 


---------- SETTING:  VALUE ----------

   Input directory :  /home/bicro/Desktop/user_folders/Tomek/microscopy_pipeline/IMR90_iTK226-241_080618/Data_input_iTK226_233
  Output directory :  /home/bicro/Desktop/user_folders/Tomek/microscopy_pipeline/IMR90_iTK226-241_080618/Data_output_iTK226_233
          Log file :  /home/bicro/Desktop/user_folders/Tomek/microscopy_pipeline/IMR90_iTK226-241_080618/Data_output_iTK226_233/2018-06-08_22:17:31_pyGPSeq.log
  
     Skipped steps :  None
  
      DNA channels :  ('dapi',)
   Signal channels :  ('cy5',)

      Segmentation :  3d
          Analysis :  mid
    Middle section :  largest
       Center perc :  True

Voxel aspect (ZYX) :  (300.0, 216.6, 216.6)
       Aspect unit :  nm
 Minimum Z portion :  0.25
    Minimum radius :  10.00 vx
        Fill holes :  True

    Sigma (smooth) :  0.0500
   Sigma (density) :  0.1000
             #bins :  200

  Condition descr. :  *NONE*

 Nuclear selection :  flat_size sumI

           Threads :  36
              Note :  TK GPSeq YFISH asynch IMR90 deconvolved, center as percentile

            Regexp :  '^(?P<channel_name>[^/]*)\.(?P<channel_id>channel[0-9]+)\.(?P<series_id>series[0-9]+)(?P<ext>(_cmle)?\.tif)$'

   Rescale deconv. :  True
   Normalize dist. :  True
         Debug mod :  False


Traceback (most recent call last):
  File "/usr/local/bin/gpseq_anim", line 6, in <module>
    exec(compile(open(__file__).read(), __file__, 'exec'))
  File "/home/bicro/Desktop/ggcode/pygpseq/bin/gpseq_anim", line 381, in <module>
    OH.write("@%s\n\n" % datetime.datetime.now())
NameError: name 'datetime' is not defined

What did you expect to happen?

to run GPSeq microscopy pipeline

What happened instead?

Didnt start running

Additional information

[ggirelli]

Wrong repo. This issue relates to pygpseq, not gpseqc. Also, bug already fixed in previous versions. Please update as explained here. Closing the ticket.