{bio}[GCCcore/12.2.0] Gubbins v3.3.5, rapidNJ v2.3.3, FastTree v2.1.11, ...

easybuild/easyconfigs/a/Autoconf-archive/Autoconf-archive-2023.02.20-GCCcore-12.2.0.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 <rob.qiao@flinders.edu.au>
+# 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': '12.2.0'}
+
+source_urls = [GNU_SOURCE]
+sources = [SOURCELOWER_TAR_XZ]
+checksums = ['71d4048479ae28f1f5794619c3d72df9c01df49b1c628ef85fde37596dc31a33']
+
+builddependencies = [
+    ('binutils', '2.39'),
+    ('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/f/FastTree/FastTree-2.1.11-GCCcore-12.2.0.eb

@@ -0,0 +1,42 @@
+# Updated from previous config
+# Author: Pavel Grochal (INUITS)
+# License: GPLv2
+
+easyblock = 'CmdCp'
+
+name = 'FastTree'
+version = '2.1.11'
+
+homepage = 'http://www.microbesonline.org/fasttree/'
+description = """FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide
+ or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of
+ time and memory. """
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+toolchainopts = {'openmp': True}
+
+# HTTPS cert error:
+# hostname 'www.microbesonline.org' doesn't match either of 'genomics.lbl.gov', 'mojave.qb3.berkeley.edu', ...
+source_urls = ['http://www.microbesonline.org/fasttree/']
+sources = [{'filename': '%(name)s-%(version)s.c', 'extract_cmd': 'cp %s FastTree.c'}]
+checksums = ['9026ae550307374be92913d3098f8d44187d30bea07902b9dcbfb123eaa2050f']
+
+builddependencies = [('binutils', '2.39')]
+
+cmds_map = [('%(name)s-%(version)s.c', '$CC -DOPENMP $CFLAGS $LIBS %%(source)s -o %(name)s')]
+
+files_to_copy = [(['FastTree'], 'bin')]
+
+# as FastTree is built with OpenMP, the correct binary is FastTreeMP
+# the FastTree binary should normally be built without OpenMP, but let’s keep it as is for backward compatibility
+# see http://www.microbesonline.org/fasttree/#OpenMP
+postinstallcmds = ['cd %(installdir)s/bin && ln -s FastTree FastTreeMP']
+
+sanity_check_paths = {
+    'files': ['bin/FastTree'],
+    'dirs': [],
+}
+
+sanity_check_commands = ['FastTree 2>&1 | grep "FastTree Version %(version)s"']
+
+moduleclass = 'bio'

easybuild/easyconfigs/g/Gubbins/Gubbins-3.3.5-foss-2022b.eb

@@ -0,0 +1,64 @@
+# 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': '2022b'}
+
+source_urls = ['https://github.com/nickjcroucher/gubbins/archive/refs/tags/']
+sources = ['v%(version)s.tar.gz']
+
+builddependencies = [
+    ('Autotools', '20220317'),
+    ('Autoconf-archive', '2023.02.20'),
+    ('pkgconf', '1.9.3'),
+    ('Check', '0.15.2'),
+    ('subunit', '1.4.3'),
+]
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('Biopython', '1.81'),
+    ('DendroPy', '4.5.2'),
+    ('numba', '0.58.1'),
+    ('SciPy-bundle', '2023.02'),
+    ('FastTree', '2.1.11'),
+    ('IQ-TREE', '2.2.2.6'),
+    ('rapidNJ', '2.3.3'),
+    ('RAxML', '8.2.12', '-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 -c "import gubbins"',
+    'python -m pip check',
+]
+
+moduleclass = 'bio'

easybuild/easyconfigs/m/multiprocess/multiprocess-0.70.15-gfbf-2022b.eb

@@ -0,0 +1,24 @@
+easyblock = 'PythonPackage'
+
+name = 'multiprocess'
+version = '0.70.15'
+
+homepage = 'https://github.com/uqfoundation/multiprocess'
+description = "better multiprocessing and multithreading in python"
+
+toolchain = {'name': 'gfbf', 'version': '2022b'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['f20eed3036c0ef477b07a4177cf7c1ba520d9a2677870a4f47fe026f0cd6787e']
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('dill', '0.3.7'),
+    ('Arrow', '11.0.0'),  # if needed rebuild --from-pr 19758
+]
+
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+moduleclass = 'lib'

easybuild/easyconfigs/r/rapidNJ/rapidNJ-2.3.3-GCCcore-12.2.0.eb

@@ -0,0 +1,41 @@
+# This seems to be actively maintained version of the code by the looks of it. 
+# See issue #5
+# https://github.com/somme89/rapidNJ/issues/5
+# why -march=native will not be used
+# Author: J. Sassmannshausen (Imperial College London/UK)
+
+easyblock = 'MakeCp'
+
+name = 'rapidNJ'
+version = '2.3.3'
+
+homepage = 'https://github.com/somme89/rapidNJ'
+description = """RapidNJ is an algorithmic engineered implementation of canonical 
+neighbour-joining. It uses an efficient search heuristic to speed-up the core 
+computations of the neighbour-joining method that enables RapidNJ to 
+outperform other state-of-the-art neighbour-joining implementations."""
+
+citing = """Rapid Neighbour Joining. Martin Simonsen, Thomas Mailund and Christian N. S. Pedersen.
+In: Proceedings of the 8th Workshop in Algorithms in Bioinformatics (WABI), LNBI 5251, 113-122,
+Springer Verlag, October 2008.
+doi: 10.1007/978-3-540-87361-7_10"""
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+source_urls = ['https://github.com/somme89/rapidNJ/archive/']
+sources = [{'filename': 'v%(version)s.tar.gz', 'download_filename': 'latest.tar.gz'}]
+checksums = ['662f864cc3e5bc68aea23129f02e0062cac9ebd37e414b54c5c5e616ff4f245d']
+
+builddependencies = [('binutils', '2.39')]
+
+files_to_copy = [(['bin/rapidnj'], 'bin')]
+
+# That is returning 1 instead of 0, so disabled for now
+# sanity_check_commands = ['rapidnj --help']
+
+sanity_check_paths = {
+    'files': ['bin/rapidnj'],
+    'dirs': [],
+}
+
+moduleclass = 'bio'