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install: homebrew hmmer2 was renamed, no longer needs binary name fix
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Signed-off-by: Kai Blin <[email protected]>
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kblin committed Dec 25, 2024
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Expand Up @@ -162,28 +162,14 @@ brew tap brewsci/bio
```
then install the binaries themselves
```bash
brew install hmmer2 hmmer diamond fasttree prodigal blast
brew install brewsci/bio/hmmer@2 hmmer diamond fasttree prodigal blast
```
For versions older than 8.0, add `brewsci/science/glimmerhmm` if you want to support fungal gene detection, but we
strongly recommend using a purpose-built fungal gene finding tool instead.

Versions older than 7.0 also need `muscle`, but homebrew only ships version 5 of that tool which no longer supports
the features antiSMASH requires `muscle` for. We recommend using a more recent antiSMASH or building muscle from source.

Unfortunately, Homebrew doesn't fix the file name conflicts between the hmmer and hmmer2 packages,
so to have both tools available, run the following:
```bash
export HMMER2_BINDIR="$(brew --prefix)/opt/hmmer2/bin"
export BREW_BINDIR="$(dirname $(brew link -n hmmer2 | head -n2 | tail -n1))"
pushd ${BREW_BINDIR}
for FNAME in ${HMMER2_BINDIR}/*; do
BINARY=$(basename $FNAME)
ln -s $FNAME ${BINARY/hmm/hmm2}
done
popd
unset HMMER2_BINDIR BREW_BINDIR
```

If you want to use CASSIS or the full RODEO analysis for RiPPs and agree to the [MEME license](http://meme-suite.org/doc/copyright.html), run
```bash
brew install https://raw.githubusercontent.com/brewsci/homebrew-bio/12b4ef4679c5c6ed21ab7c046c2709c4cefb4338/Formula/meme.rb
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