ParBLiSS / FastANI

Fast Whole-Genome Similarity (ANI) Estimation
Apache License 2.0
374 stars 67 forks source link

Problem with M1 chip installation #112

Open GM110Z opened 1 year ago

GM110Z commented 1 year ago

Hello

I have tried to install fastANI on my mac with M1 chip but I received the following error: src/cgi/core_genome_identity.cpp:11:10: fatal error: 'omp.h' file not found

I followed various threads here in the issues page and as suggested I tried to install libomp but the issue was not solved and the error remained. I even tried to install by conda but in that case I got the error '/usr/lib/libgsl.25.dylib' (no such file, not in dyld cache)

Then tried by brew but the error I got in this case was checking for boost/math/distributions/binomial.hpp... no configure: error: Boost Library headers not found.

Any idea how I could bypass any of the problems so I could use fastANI?

apbouwens commented 1 year ago

I was able to compile fastANI on my MacBookPro M1 (2020) using the following steps:

I used brew to install libomp and gsl:

brew install libomp gsl

Then followed the installation instructions: ./bootstrap.sh ./configure --with-gsl=/opt/homebrew/opt/gsl

Before running make, I edited the Makefile:

Finally, I ran make successfully.

GM110Z commented 1 year ago

Thank you that worked!

lm-jkominek commented 1 year ago

Run into the similar issue on my 2020 Intel Mac, running Ventura 13.1. Your answer helped, but the homebrew paths were different- instead of "/opt/homebrew/opt/" my machine used "/usr/local/opt/", just thought I'd share.