{bio}[GCCcore/12.3.0] Gubbins v3.3.5, SKA2 v0.3.7, RAxML v8.2.12, ... w/ hybrid avx2

easybuild/easyconfigs/a/Autoconf-archive/Autoconf-archive-2023.02.20-GCCcore-12.3.0.eb

@@ -0,0 +1,53 @@
+##
+# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia
+# Homepage: 	https://staff.flinders.edu.au/research/deep-thought
+#
+# Authors::	Robert Qiao <[email protected]>
+# License::	GNU Free Documentation License
+#
+# Notes::
+##
+
+easyblock = 'ConfigureMake'
+
+name = 'Autoconf-archive'
+version = '2023.02.20'
+
+homepage = "https://www.gnu.org/software/autoconf-archive"
+
+description = """
+The GNU Autoconf Archive is a collection of more than 500 macros for GNU Autoconf
+that have been contributed as free software by friendly supporters of the cause from
+all over the Internet. Every single one of those macros can be re-used without
+imposing any restrictions whatsoever on the licensing of the generated configure script.
+In particular, it is possible to use all those macros in configure scripts that
+are meant for non-free software. This policy is unusual for a Free Software Foundation
+project. The FSF firmly believes that software ought to be free, and software licenses
+like the GPL are specifically designed to ensure that derivative work based on free
+software must be free as well. In case of Autoconf, however, an exception has been made,
+because Autoconf is at such a pivotal position in the software development tool chain
+that the benefits from having this tool available as widely as possible outweigh the
+disadvantage that some authors may choose to use it, too, for proprietary software.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = [GNU_SOURCE]
+sources = [SOURCELOWER_TAR_XZ]
+checksums = ['71d4048479ae28f1f5794619c3d72df9c01df49b1c628ef85fde37596dc31a33']
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('Autotools', '20220317'),
+    ('makeinfo', '7.0.3'),
+]
+
+preconfigopts = 'autoreconf -i -f &&'
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['share/%s' % x for x in
+             ['aclocal', 'doc', 'info']],
+}
+
+moduleclass = 'devel'

easybuild/easyconfigs/g/Gubbins/Gubbins-3.3.5-foss-2023a.eb

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+# This easyconfig was created by the BEAR Software team at the University of Birmingham.
+easyblock = 'ConfigureMake'
+
+name = 'Gubbins'
+version = '3.3.5'
+
+homepage = "https://nickjcroucher.github.io/gubbins/"
+description = """Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that
+ iteratively identifies loci containing elevated densities of base substitutions, which are marked as recombinations,
+ while concurrently constructing a phylogeny based on the putative point mutations outside of these regions.
+ Simulations demonstrate the algorithm generates highly accurate reconstructions under realistic models of short-term
+ bacterial evolution, and can be run in only a few hours on alignments of hundreds of bacterial genome sequences."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+source_urls = ['https://github.com/nickjcroucher/gubbins/archive/refs/tags/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['4ee363f82708bdda0c00d1c6c334cf20127bd852ee488619f61140771a279774']
+
+builddependencies = [
+    ('Autotools', '20220317'),
+    ('Autoconf-archive', '2023.02.20'),
+    ('pkgconf', '1.9.5'),
+    ('Check', '0.15.2'),
+    ('subunit', '1.4.4'),
+]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Biopython', '1.83'),
+    ('DendroPy', '4.6.1'),
+    ('numba', '0.58.1'),
+    ('SciPy-bundle', '2023.07'),
+    ('FastTree', '2.1.11'),
+    ('IQ-TREE', '2.3.5'),
+    ('rapidNJ', '2.3.3'),
+    ('RAxML', '8.2.12', '-hybrid-avx2'),
+    ('RAxML-NG', '1.2.0'),
+    ('SKA2', '0.3.7'),
+    ('dill', '0.3.7'),
+    ('multiprocess', '0.70.15'),
+]
+
+preconfigopts = "autoreconf -i && "
+# runtest = 'check'  # runs the Python tests and this causes package to be installed into the Python install
+postinstallcmds = [
+    """sed -i 's/self.executable = "iqtree"/self.executable = "iqtree2"/' python/gubbins/treebuilders.py""",
+    "cd python && python -m pip install --prefix %(installdir)s --no-build-isolation . "
+]
+
+modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'}
+
+sanity_check_paths = {
+    'files': ['bin/gubbins', 'lib/libgubbins.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+sanity_check_commands = [
+    "gubbins --help",
+    "run_gubbins.py --version",
+    'python -s -c "import gubbins"',
+    'PIP_DISABLE_PIP_VERSION_CHECK=true python -s -m pip check',
+]
+
+moduleclass = 'bio'

easybuild/easyconfigs/r/RAxML/RAxML-8.2.12-gompi-2023a-hybrid-avx2.eb

@@ -0,0 +1,30 @@
+easyblock = 'MakeCp'
+
+name = 'RAxML'
+version = '8.2.12'
+versionsuffix = '-hybrid-avx2'
+
+homepage = 'https://github.com/stamatak/standard-RAxML'
+description = "RAxML search algorithm for maximum likelihood based inference of phylogenetic trees."
+
+toolchain = {'name': 'gompi', 'version': '2023a'}
+toolchainopts = {'usempi': True}
+
+source_urls = ['https://github.com/stamatak/standard-RAxML/archive/']
+sources = ['v%(version)s.zip']
+checksums = ['abe6978c6027e897ebed67066836e4eadd57ecd0d042045634424dd001e86105']
+
+buildopts = '-f Makefile.AVX2.HYBRID.gcc CC="$CC"'
+
+files_to_copy = [(["raxmlHPC-HYBRID-AVX2"], "bin"), "usefulScripts", "README", "manual"]
+
+postinstallcmds = ["cd %(installdir)s/bin && ln -s raxmlHPC-HYBRID-AVX2 raxmlHPC"]
+
+sanity_check_paths = {
+    'files': ['bin/raxmlHPC'],
+    'dirs': [],
+}
+
+sanity_check_commands = ["raxmlHPC -%s" % x for x in ['h', 'v']]
+
+moduleclass = 'bio'