From c97cca99c1275127a97867dfff57256bd9486d8b Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Thu, 28 Mar 2024 18:45:41 +0100 Subject: [PATCH 1/4] Update Compilation-Guide.md with `--recursive` clone and ARM flag Relates to https://github.com/iqtree/iqtree2/issues/153 Relates to https://github.com/iqtree/iqtree2/issues/169 --- doc/Compilation-Guide.md | 10 ++-------- 1 file changed, 2 insertions(+), 8 deletions(-) diff --git a/doc/Compilation-Guide.md b/doc/Compilation-Guide.md index dee7490..b18c9a5 100644 --- a/doc/Compilation-Guide.md +++ b/doc/Compilation-Guide.md @@ -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: @@ -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 . 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 ----------------------- From 1468dcd7b81509260ff6cf78dfc5fb21eb09dfe8 Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Thu, 28 Mar 2024 18:47:29 +0100 Subject: [PATCH 2/4] Remove reference to homebrew science, as that tap is deprecated See https://github.com/brewsci/homebrew-science for deprecation notice --- doc/Compilation-Guide.md | 3 --- 1 file changed, 3 deletions(-) diff --git a/doc/Compilation-Guide.md b/doc/Compilation-Guide.md index b18c9a5..16aab60 100644 --- a/doc/Compilation-Guide.md +++ b/doc/Compilation-Guide.md @@ -115,9 +115,6 @@ Compiling under Mac OS X ------------------------
->**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} - * Make sure that Clang compiler is installed, which is typically the case if you installed Xcode and the associated command line tools. * If you installed cmake with Homebrew From cb45924db4e9316ef46b9b9514091d1cf2a03d7c Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Thu, 28 Mar 2024 18:51:55 +0100 Subject: [PATCH 3/4] Update homebrew tap --- doc/Compilation-Guide.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/doc/Compilation-Guide.md b/doc/Compilation-Guide.md index 16aab60..576c250 100644 --- a/doc/Compilation-Guide.md +++ b/doc/Compilation-Guide.md @@ -115,6 +115,9 @@ Compiling under Mac OS X ------------------------
+>**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 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. * If you installed cmake with Homebrew From 88f1be42cf9fc9c40e88a094cf9c2bc71916823f Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Thu, 28 Mar 2024 18:52:16 +0100 Subject: [PATCH 4/4] !fixup --- doc/Compilation-Guide.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/Compilation-Guide.md b/doc/Compilation-Guide.md index 576c250..618fd2f 100644 --- a/doc/Compilation-Guide.md +++ b/doc/Compilation-Guide.md @@ -115,7 +115,7 @@ Compiling under Mac OS X ------------------------
->**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 brew install brewsci/bio/iqtree2` to install. +>**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.