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update doc
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sgalvagno committed Jan 14, 2025
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Expand Up @@ -9,7 +9,6 @@ A pipeline tool to convert Cytosense data files to EcoTaxa compatible format.
- Automated conversion from Cytosense (.cyz) to EcoTaxa format
- Built-in cyz2json binary for data extraction
- Cross-platform support (Linux, Windows, MacOS)
- System-wide installation

# pre installation
## Linux
Expand All @@ -36,11 +35,13 @@ on Windows use install.ps1 instead of install.sh not tested


### On MacOSX
manual build
to bypass security with xattr command, then need to go in Systems Settings > Security & Privacy > General and allow the app to be opened for the 10+ libraries. (need to relauch sevaral time the cyz2json binary)

or use
When you use manual build: you need to bypass security
You have 2 possibilities :
using xattr command.
```
xattr -d com.apple.quarantine /opt/cytosense_to_ecotaxa_pipeline/bin/*
```
or if you do not want use xattr you need to go in Systems Settings > Security & Privacy > General and allow the app to be opened for the 10+ libraries. You need to relauch sevaral time the cyz2json binary to acheive all neccessary permissions.


# Run the pipeline
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