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Update Compilation-Guide.md with --recursive clone and ARM flag #3

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Update Compilation-Guide.md with --recursive clone and ARM flag #3

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c97cca9
Update Compilation-Guide.md with `--recursive` clone and ARM flag
corneliusroemer Mar 28, 2024
1468dcd
Remove reference to homebrew science, as that tap is deprecated
corneliusroemer Mar 28, 2024
cb45924
Update homebrew tap
corneliusroemer Mar 28, 2024
88f1be4
!fixup
corneliusroemer Mar 28, 2024
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12 changes: 3 additions & 9 deletions doc/Compilation-Guide.md
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Expand Up @@ -66,7 +66,7 @@ For IQ-TREE version 1 please use:

Alternatively, if you have `git` installed, you can also clone the source code from GitHub with:

git clone https://github.com/iqtree/iqtree2.git
git clone --recursive https://github.com/iqtree/iqtree2.git

For IQ-TREE version 1 please clone:

Expand Down Expand Up @@ -115,7 +115,7 @@ Compiling under Mac OS X
------------------------
<div class="hline"></div>

>**TIP**: A ready made IQ-TREE package is provided by * [Homebrew](https://github.com/brewsci/homebrew-science/blob/master/Formula/iqtree.rb) by simply running `brew install homebrew/science/iqtree2`.
>**TIP**: A ready made IQ-TREE package is provided via the * [Homebrew tap brewsci/bio](https://github.com/brewsci/homebrew-bio/blob/master/Formula/iqtree2.rb). Simply run `brew install brewsci/bio/iqtree2` to install.
{: .tip}

* Make sure that Clang compiler is installed, which is typically the case if you installed Xcode and the associated command line tools.
Expand All @@ -126,16 +126,10 @@ Compiling under Mac OS X

The steps to compile IQ-TREE are similar to Linux (see above), except that you need to specify `clang` as compiler when configuring source code with CMake (step 4):

cmake -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ ..
cmake -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_CXX_FLAGS="-Dthread_local=" ..

(please change `cmake` to absolute path like `/Applications/CMake.app/Contents/bin/cmake`).

To compile the multicore version, the default installed Clang unfortunately does not support OpenMP (which might change in the near future). However, the latest Clang 3.7 supports OpenMP, which can be downloaded from <http://clang.llvm.org>. After that you can run CMake with:

cmake -DIQTREE_FLAGS=omp -DCMAKE_C_COMPILER=clang-3.7 -DCMAKE_CXX_COMPILER=clang++-3.7 ..

(assuming that `clang-3.7` and `clang++-3.7` points to the installed Clang 3.7).


Compiling under Windows
-----------------------
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