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I'm pretty new to bioinformatics, I got some shell scripts from a senior who used to do things that I need to do, but these scripts were written on a Mac and I'm trying to set it up for Windows, through git bash.

I have trouble with running the MAFFT package though. I installed MAFFT Ubuntu version for Windows (https://mafft.cbrc.jp/alignment/software/ubuntu_on_windows.html) and was able to run it on the Ubuntu app, but don't know if there's an easy way to run MAFFT on git bash directly, or somehow call the Ubuntu app through git bash to run MAFFT?

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  • $\begingroup$ Not sure it will fit your question, but I heard you better use powershell to run shell script on windows. stackoverflow.com/questions/1098786/…. From the comments of the answer in this linked question, installing Git on windows optionnally add UNIX tools to powershell $\endgroup$ – Paul Endymion Nov 21 '19 at 16:17

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