How do you install ExpansionHunterDenovo on a Mac?
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6 weeks ago

I'm trying to install ExpansionHunterDenovo on my Mac. It says it should be compatible here:

https://github.com/Illumina/ExpansionHunterDenovo/blob/master/documentation/02_Installation.md

However, I don't seem to be able to get it to work. Here are my steps:

cd bin/
    wget wget https://github.com/Illumina/ExpansionHunterDenovo/releases/download/v0.9.0/ExpansionHunterDenovo-v0.9.0-linux_x86_64.tar.gz
    tar -zxvf ExpansionHunterDenovo-v0.9.0-linux_x86_64.tar.gz
    cd ExpansionHunterDenovo-v0.9.0-linux_x86_64/bin
    chmod +x ExpansionHunterDenovo # Make executable
    mv ExpansionHunterDenovo /Users/michaelflower/bin # Move to bin so it's in my PATH
ExpansionHunterDenovo --version
-bash: /Users/michaelflower/bin/ExpansionHunterDenovo: cannot execute binary file
ExpansionHunterDenovo • 340 views
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Entering edit mode

You're downloading the linux_x86_64 binary on a Mac. That's why it doesn't work. Look for a macOS binary or compile from source.

EDIT: The page says it's supposed to work on both Linux and macOS but that page was updated 4 years ago. I'd say go ahead and try compiling from source and also raise an issue on that repository.

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Entering edit mode

Thanks. This page suggests it can be installed with conda.

https://bioconda.github.io/recipes/expansionhunterdenovo/README.html

conda install bioconda::expansionhunterdenovo

But I still get an error with it

error    libmamba Could not solve for environment specs
    The following package could not be installed
     expansionhunterdenovo does not exist (perhaps a typo or a missing channel).
critical libmamba Could not solve for environment specs

However, expansionhunter installs fine

https://anaconda.org/bioconda/expansionhunter

conda install bioconda::expansionhunter

But I still need ExpansionHunterDenovo

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Entering edit mode

Like I said, try compiling from source and check the repo's issues. From a preliminary glance, this looks like abandonware but I could be wrong.

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