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angelolab / ark-analysis

Integrated pipeline for multiplexed image analysis
https://ark-analysis.readthedocs.io/en/latest/
MIT License
71 stars 25 forks source link

Issue setting up the repo on Windows #1004

Closed jlqm2 closed 1 year ago

jlqm2 commented 1 year ago

I'm trying to set up the repo on Windows and I keep getting the following error when I run "bash start_docker.sh":

C:\Users\jlqm2\ark-analysis>bash start_docker.sh start_jupyter.sh: line 8: syntax error: unexpected end of file

srivarra commented 1 year ago

The bash scripts need to be converted with the dos2unix tool installed using wsl. Once you have wsl and dos2unix you will need to run the following command wsl dos2unix for start_docker.sh update_notebooks.sh and start_jupyter.sh respectively. Then will be able to run start_docker.sh successfully.

We have some documentation here which goes over installing wsl / docker, converting the bash scripts.

julienmortier commented 1 year ago

I had the same issue as Jlqm2 and it was fixed by running "wsl dos2unix start_jupyter.sh" as srivarra suggested. However, this is not mentioned in the documentation for Windows configuration and is also not mentioned in the youtube video (https://www.youtube.com/watch?v=EXMGdi_Izdw&t=1s).

srivarra commented 1 year ago

@julienmortier Thanks for pointing that out, the docs will be updated in #1012.