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Cannot install bwa-mem2 via conda

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I cannot seem to figure out what is going on, have also tried installing with mamba, installing in a new environment, updating/downgrading various packages to see if that was causing issues, restarted mac as well. any help is appreciated. Always seems to return some variation of the same error failing to solve the environment.

conda mamba python
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updated by Ram Ram • written by jsmith120f • jsmith120f

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updated by Ram Ram • written by Pierre Lindenbaum Pierre Lindenbaum

1 answer

The problem is caused by running the ARM-based conda. Bioinformatics software is compiled for Intel based CPUs only.

Uninstall that version of conda and install and run the osx-64 (Intel CPU) based conda even on an osx-arm64 (M processor) based MacOS

Use micromamba actually, it is much simpler, faster and usable than conda/mamba

You need to do this:

# macOS Intel (x86_64):
curl -Ls https://micro.mamba.pm/api/micromamba/osx-64/latest | tar -xvj bin/micromamba

then use micromamba instead of conda from that moment on.

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written by Istvan Albert Istvan Albert

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