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BodenmillerGroup / ImcSegmentationPipeline

A pixel classification based multiplexed image segmentation pipeline
https://bodenmillergroup.github.io/ImcSegmentationPipeline/
MIT License
83 stars 35 forks source link

Error Processing imctools in Conda #2

Closed halbrindley closed 5 years ago

halbrindley commented 6 years ago

Hi guys,

When trying to load the IMCTools environment in Conda the following error message appears without loading the environment. Any suggestions would be greatly appreciated! Thank you for your help.

ScannerError(None, None, 'mapping values are not allowed here', <ruamel_yaml.error.StringMark object at 0x000001F8FA0782A0>)

votti commented 6 years ago

Hi there!

The error indicates that there is a formatting mistake in the conda_imctools.yml file - however I never observed this when testing this from either Ubuntu or Windows. Did you happen to change something in that file (e.g. the name of the environment)? Already an additional space at the wrong place might be enough to break things.

An you maybe open your conda_imctools.yml in a text editor and copy paste the content into: https://codebeautify.org/yaml-validator and use validate to check whether there is any obvious mistake?

Also could you indicate: Which operation system are you using? Are you using the conda command line or the GUI user interface?

Cheers, Vito

halbrindley commented 6 years ago

Hi Vito,

Thanks for the rapid reply. Also thanks for the suggestion; the downloaded .yml file from GitHub included html coding rather than the intended script. I copied the text from the RAW format off GitHUb and then pasted into text editor Notepad++ and saved it as a new .yml file. Now it has successfully loaded the environment. I am using Windows 10 Pro with Anaconda GUI interface.

Many Thanks

Hal

votti commented 5 years ago

Cool! Let me know if something else is unclear/not working in the current description! Hopefully will be able to release a new version incorporating the feedback next week.