nproc: command not found make[1]: *** [process] Error 127

wbaopaul / scATAC-pro

A comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data

MIT License

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nproc: command not found make[1]: *** [process] Error 127 #21

Closed sylestiel closed 4 years ago

sylestiel commented 4 years ago

/usr/local/bin/scATAC-pro_1.1.4/scripts/trimming.sh: line 20: nproc: command not found make[1]: *** [process] Error 127

wbaopaul commented 4 years ago

nproc is not supportted by mac; I guess there are many other commands not support by mac OS. I will try to adjust those commands compatible for mac OS but may not have enough time to adjust all in a short time. Please switch to a linux server or HPC or using docker or singularity version. Generally, it's not recommend to run scatac-pro on mac pc; there are many module (like the mapping module) requires very large memory, so I geuss it's not realistic to run it on mac pc anyway.

wbaopaul commented 4 years ago

For this specific issue, you can add run alias nproc="sysctl -n hw.logicalcpu" in your terminal before you run scatac-pro on your mac.

sylestiel commented 4 years ago

Thank you. Looking forward to a mac compatible command line.