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NameError in line 134 of Skipper.py: name 'directory' is not defined File "Skipper.py", line 134, in <module> #14

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MSajek opened this issue Sep 13, 2023 · 6 comments

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@MSajek
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MSajek commented Sep 13, 2023

Hi,
I try to run skipper on eCLIP data (not from ENCODE). I prepared proper environment with all dependencies, config file and manifest and when run:
snakemake -ns ~/programs/skipper/Skipper.py -j 1
I have the following error:
NameError in line 134 of Skipper.py: name 'directory' is not defined File "Skipper.py", line 134, in <module>
It looks like directory() declaration is not recognized for some reasons.
When I commented line 134 I have the next error:
InputFunctionException in line 541 of Skipper.py: KeyError: '{experiment_label}' Wildcards: experiment_label={experiment_label}
Any suggestions how to solve these issues will be helpful.
I also suggest to add toy dataset to repo to make some tests before running on new data.
Best,
Marcin

@augustboyle
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augustboyle commented Sep 13, 2023 via email

@MSajek
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MSajek commented Sep 13, 2023

Hi Evan,
Thanks, I will download and try to run on suggested data. However errors themselves look like data independent. Any suggestions how to fix them? It can be helpful if you can post not only the list of required dependencies but also their versions.
Best,
Marcin

@augustboyle
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augustboyle commented Sep 13, 2023 via email

@MSajek
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MSajek commented Sep 17, 2023

Hi Evan,
The same error:
InputFunctionException in line 541 of Skipper.py: KeyError: '{experiment_label}' Wildcards: experiment_label={experiment_label}
occurs with your manifest file, where I only replaced paths to files
When I started to checking Skipper.py line by line everything was looking ok and I have no idea why I have this error.

@augustboyle
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augustboyle commented Nov 16, 2023 via email

@MSajek
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MSajek commented Nov 16, 2023

Unfortunately I don't. I tried a few things and nothing worked. I decided to run skipper script by script and then everything works fine.

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