Merge pull request #20955 from TopRichard/IQtree-inc-patch

{bio}[gompi/2023a] IQ-TREE v2.3.5

easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.3.5-gompi-2023a.eb

@@ -0,0 +1,55 @@
+# Updated to v2.1.3 by
+# R.QIAO <[email protected]>
+# DeepThought, Flinders University
+
+easyblock = 'CMakeMake'
+
+name = 'IQ-TREE'
+version = '2.3.5'
+
+# HTTPS is not working
+homepage = 'http://www.iqtree.org/'
+description = """Efficient phylogenomic software by maximum likelihood"""
+
+toolchain = {'name': 'gompi', 'version': '2023a'}
+# Including 'usempi' will take precedence and override IQTREE_FLAGS and produces only 'iqtree-mpi' binary
+
+source_urls = ['https://github.com/iqtree/iqtree2/archive/refs/tags/']
+sources = ['v%(version)s.tar.gz']
+patches = [
+    'IQ-TREE-2.3.5_use_EB_LSD2.patch',
+]
+checksums = [
+    {'v2.3.5.tar.gz': '8e323e0b7c46e97901d3500f11e810703e0e5d25848188047eca9602d03fa6b1'},
+    {'IQ-TREE-2.3.5_use_EB_LSD2.patch': 'b4578b01f06ae52b94b332622c0f6630497cd29cb61010f58f7c5018c2c32a5f'},
+]
+
+builddependencies = [
+    ('CMake', '3.26.3'),
+    ('Eigen', '3.4.0'),
+]
+dependencies = [
+    ('zlib', '1.2.13'),
+    ('Boost', '1.82.0'),
+    ('LSD2', '2.4.1'),
+]
+
+local_conf_opts = ' -DUSE_LSD2=ON '
+configopts = [
+    '-DIQTREE_FLAGS=omp' + local_conf_opts,
+    '-DIQTREE_FLAGS=mpi -DCMAKE_C_COMPILER="$MPICC" -DCMAKE_CXX_COMPILER="$MPICXX"' + local_conf_opts,
+]
+
+sanity_check_paths = {
+    'files': ['bin/iqtree2', 'bin/iqtree2-mpi'],
+    'dirs': [],
+}
+
+sanity_check_commands = [
+    "iqtree2 --help",
+    "mkdir -p $TMPDIR/{test-omp,test-mpi}",
+    "cd $TMPDIR/test-omp && cp -a %(installdir)s/example.phy . && iqtree2 -s example.phy -redo",
+    "cd $TMPDIR/test-mpi && cp -a %(installdir)s/example.phy . && mpirun -np 1 iqtree2-mpi -s example.phy -redo",
+]
+
+moduleclass = 'bio'

easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.3.5_use_EB_LSD2.patch

@@ -0,0 +1,36 @@
+diff -ruN iqtree2-2.3.5/CMakeLists.txt iqtree2-2.3.5-orig/CMakeLists.txt
+--- iqtree2-2.3.5/CMakeLists.txt	2024-06-26 04:33:33.000000000 +0000
++++ iqtree2-2.3.5-orig/CMakeLists.txt	2024-07-03 08:23:41.030462539 +0000
+@@ -758,10 +758,6 @@
+    add_subdirectory(terracetphast)
+ endif()
+
+-if (USE_LSD2)
+-    add_subdirectory(lsd2)
+-endif()
+-
+ add_library(kernelsse tree/phylokernelsse.cpp)
+
+ if (NOT BINARY32 AND NOT IQTREE_FLAGS MATCHES "novx")
+@@ -820,9 +816,6 @@
+         if (USE_TERRAPHAST)
+             set_target_properties(terracetphast terraphast PROPERTIES COMPILE_FLAGS "${SSE_FLAGS}")
+         endif()
+-        if (USE_LSD2)
+-            set_target_properties(lsd2 PROPERTIES COMPILE_FLAGS "${SSE_FLAGS}")
+-        endif()
+         if (USE_BOOSTER)
+             set_target_properties(booster PROPERTIES COMPILE_FLAGS "${SSE_FLAGS}")
+         endif()
+diff -ruN iqtree2-2.3.5/main/timetree.cpp iqtree2-2.3.5-orig/main/timetree.cpp
+--- iqtree2-2.3.5/main/timetree.cpp	2024-06-26 04:33:33.000000000 +0000
++++ iqtree2-2.3.5-orig/main/timetree.cpp	2024-07-03 08:24:32.438606710 +0000
+@@ -8,7 +8,7 @@
+ #include "timetree.h"
+
+ #ifdef USE_LSD2
+-#include "lsd2/src/lsd.h"
++#include "lsd.h"
+ #endif
+
+ /** map from taxon name to date */