adding easyconfigs: IQ-TREE-2.2.2.7-gompi-2023a.eb, LSD2-2.4.1-GCCcor…

…e-12.3.0.eb

easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.2.2.7-gompi-2023a.eb

@@ -0,0 +1,57 @@
+# Updated to v2.1.3 by
+# R.QIAO <rob.qiao@flinders.edu.au>
+# DeepThought, Flinders University
+
+easyblock = 'CMakeMake'
+
+name = 'IQ-TREE'
+version = '2.2.2.7'
+
+# 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/']
+sources = ['v%(version)s.tar.gz']
+patches = [
+    'IQ-TREE-2.1.2_use_EB_LSD2.patch',
+    'IQ-TREE-2.2.1_fix-mpi.patch',
+]
+checksums = [
+    {'v2.2.2.7.tar.gz': '407a1a56d352ba9c2152a1d708cd29db872a41c252fbdc7acd8e0de0da8af008'},
+    {'IQ-TREE-2.1.2_use_EB_LSD2.patch': 'daa2ab12d44e26eb5607c4ed6acb9d970e230a83dabcf21461f37bc48263b816'},
+    {'IQ-TREE-2.2.1_fix-mpi.patch': '9ead6808efd11d4c01dd265cca6094cffd6377746d3b2fc84b43d2faeee0777c'},
+]
+
+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/l/LSD2/LSD2-2.4.1-GCCcore-12.3.0.eb

@@ -0,0 +1,40 @@
+# Updated to v2.3 by
+# R.QIAO <rob.qiao@flinders.edu.au>
+# DeepThought, Flinders University
+
+easyblock = 'CMakeMake'
+
+name = 'LSD2'
+version = '2.4.1'
+
+homepage = 'https://github.com/tothuhien/lsd2'
+description = "Least-squares methods to estimate rates and dates from phylogenies"
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+github_account = 'tothuhien'
+
+source_urls = [GITHUB_LOWER_SOURCE]
+sources = ['v.%(version)s.tar.gz']
+patches = ['%(name)s-1.9.7_fix_cmake_to_build_lib_and_binary.patch']
+checksums = [
+    {'v.2.4.1.tar.gz': '3d0921c96edb8f30498dc8a27878a76d785516043fbede4a72eefd84b5955458'},
+    {'LSD2-1.9.7_fix_cmake_to_build_lib_and_binary.patch':
+     '8ef6e8c3a9a5aa2099678ed84a7e54ef687e3900894694c4eec1f5399f0487f6'},
+]
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('CMake', '3.26.3'),
+]
+
+build_shared_libs = True
+
+sanity_check_paths = {
+    'files': ['bin/lsd2', 'lib/liblsd2.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+sanity_check_commands = ['lsd2 -h']
+
+moduleclass = 'bio'