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skovaka / UNCALLED

Raw nanopore signal mapper that enables real-time targeted sequencing
MIT License
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Implementation on ARM64 Raspberry Pi 4 #33

Open trappaj opened 3 years ago

trappaj commented 3 years ago

Hey There!

I am trying to get Uncalled up and running in our lab on a new Raspberry Pi 4 but am running into a few problems when I go to run the setup.py. It is throwing this error when trying to compile ksw.c in the /submods/bwa:

fatal error: emmintrin.h: No such file or directory

From what I can tell the error has to do with GCC but I have not been able to find a solution yet. I was able to get it up and running on another machine, but it has a x86_64 architecture compared to the ARM64 on the Raspberry Pi.

I guess I'm asking if there has been any testing if it can be run with a ARM64 architecture, or more so on any Raspberry Pi devices. For reference I am running Ubuntu 20.10 on both machines. Any help would be appreciated!

skovaka commented 3 years ago

I have not tested UNCALLED on ARM64 architecture, and I'm not very familiar with what kind of issues come up. I found this fork of BWA which might help though: https://github.com/hasindu2008/bwa-arm. If you replace the contents of /submods/bwa with the contents of that repo that might fix the BWA issue? However, BWA is built before the actual UNCALLED code, so I wouldn't be surprised if you run into more issues down the line.

harisankarsadasivan commented 2 years ago

@trappaj Any updates on this?

skovaka commented 2 years ago

I still have not tested it, but I might be able to in a month or two. If anybody tries the suggestion above (replace the contents of submods/bwa with https://github.com/hasindu2008/bwa-arm), I'd be happy to hear how it goes!