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Using Homebrew
If you prefer to see code in action, the full installation process with homebrew is available as a Notebook in Google Colab.
You can use Homebrew to install most of the software required by MiGA. If you don't have Homebrew, execute (and follow the instructions):
/bin/bash -c "$(curl -fsSL \
https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
It's possible you already have a recent version of ruby (2.3+). To check which version you have, simply run:
ruby -v. If your version of Ruby is older than 2.3, you can install a recent version using:brew install libyaml rbenv
rbenv install 3.0.1
rbenv global 3.0.1
Now that you have Homebrew, execute:
brew tap brewsci/bio
# In Linux, replace 'temurin' with 'openjdk'
brew install \
r sqlite3 python temurin \
blast hmmer bedtools prodigal gmp idba mcl krona \
barrnap diamond fastani faqcs falco seqtk fastp trnascan
We also recommend installing the
sqlite3 gem beforehand using the brew libraries, to avoid headaches down the road (but this is optional):gem install sqlite3 -- --with-sqlite3-dir="$(brew --prefix sqlite3)"
If you want to activate the MyTaxa and MyTaxa Scan steps, follow the instructions to install the MyTaxa Utils.
Last modified 10mo ago