Merge branch 'develop' of https://github.com/easybuilders/easybuild-e…

…asyconfigs into 20240314145918_new_pr_CellRank202

easybuild/easyconfigs/a/AMOS/AMOS-3.1.0-foss-2023a.eb

@@ -23,10 +23,18 @@ toolchainopts = {'pic': True, 'cstd': 'c++98'}
 
 source_urls = [SOURCEFORGE_SOURCE]
 sources = [SOURCELOWER_TAR_GZ]
-patches = ['AMOS-%(version)s_GCC-4.7.patch']
+patches = [
+    'AMOS-%(version)s_GCC-4.7.patch',
+    'AMOS-3.1.0_fix_deprecated_maxmatch-flag.patch',
+    'AMOS-3.1.0_link_correctly_to_DELTAFILER_SHOWCOORDS.patch',
+]
 checksums = [
-    '2d9f50e39186ad3dde3d3b28cc265e8d632430657f40fc3978ce34ab1b3db43b',  # amos-3.1.0.tar.gz
-    '8633ff196568e208cc12932f25f46fa35f7e9a9e80e0bbf4288ae070dd7b8844',  # AMOS-3.1.0_GCC-4.7.patch
+    {'amos-3.1.0.tar.gz': '2d9f50e39186ad3dde3d3b28cc265e8d632430657f40fc3978ce34ab1b3db43b'},
+    {'AMOS-3.1.0_GCC-4.7.patch': '8633ff196568e208cc12932f25f46fa35f7e9a9e80e0bbf4288ae070dd7b8844'},
+    {'AMOS-3.1.0_fix_deprecated_maxmatch-flag.patch':
+     '80379cee8e8c8228590af89d37ea3fdb734c7e0ebe5bb357eaf2af71d1399fc6'},
+    {'AMOS-3.1.0_link_correctly_to_DELTAFILER_SHOWCOORDS.patch':
+     'e291d87b8cd27752474ee0e1f3acb44f9657cac50d5d6dcceca0efc6436f1fe1'},
 ]
 
 dependencies = [

easybuild/easyconfigs/a/AMOS/AMOS-3.1.0_fix_deprecated_maxmatch-flag.patch

@@ -0,0 +1,14 @@
+Replace deprecate NUCMER flag -maxmatch with --maxmatch (from MUMmer 4.0.0rc)
+see https://github.com/sanger-pathogens/circlator/issues/121 and https://github.com/mummer4/mummer/issues/49
+diff -ru amos-3.1.0.orig/src/Pipeline/minimus2.acf amos-3.1.0/src/Pipeline/minimus2.acf
+--- amos-3.1.0.orig/src/Pipeline/minimus2.acf	2011-07-25 01:27:26.000000000 +0200
++++ amos-3.1.0/src/Pipeline/minimus2.acf	2024-03-13 17:03:35.981707768 +0100
+@@ -54,7 +54,7 @@
+ 13: $(BINDIR)/dumpreads $(BANK) -m $(REFCOUNT) > $(QRYSEQ)
+
+ ## Getting overlaps 
+-20: $(NUCMER) -maxmatch -c $(OVERLAP) $(REFSEQ) $(QRYSEQ) -p $(PREFIX)
++20: $(NUCMER) --maxmatch -c $(OVERLAP) $(REFSEQ) $(QRYSEQ) -p $(PREFIX)
+ 21: $(SHOWCOORDS) -H -c -l -o -r -I $(MINID) $(ALIGN) | $(BINDIR)/nucmerAnnotate | egrep 'BEGIN|END|CONTAIN|IDENTITY' > $(COORDS) 
+ 22: $(BINDIR)/nucmer2ovl -ignore $(MAXTRIM) -tab $(COORDS) | $(BINDIR)/sort2 > $(OVLTAB)
+

easybuild/easyconfigs/a/AMOS/AMOS-3.1.0_link_correctly_to_DELTAFILER_SHOWCOORDS.patch

@@ -0,0 +1,15 @@
+minimus2 needs delta-filter and show-coords but these were not set correctly like NUCMER
+author: Lara Peeters (HPC-UGent)
+diff -ru amos-3.1.0.orig/src/Pipeline/Makefile.in amos-3.1.0/src/Pipeline/Makefile.in
+--- amos-3.1.0.orig/src/Pipeline/Makefile.in	2011-08-05 05:08:07.000000000 +0200
++++ amos-3.1.0/src/Pipeline/Makefile.in	2024-03-14 12:31:16.218067000 +0100
+@@ -477,7 +477,8 @@
+                 echo '#!$(bindir)/runAmos -C' > "$(DESTDIR)$(bindir)/$$b"; \
+                 sed -e 's|^BINDIR[ 	]*=.*$$|BINDIR=$(bindir)|' \
+                     -e 's|^NUCMER[ 	]*=.*$$|NUCMER=$(NUCMER)|' \
+-                    -e 's|^DELTAFILTER[        ]*=.*$$|DELTAFILTER=$(DELTAFILTER)|' \
++                    -e 's|^DELTAFILTER[ 	]*=.*$$|DELTAFILTER=$(DELTAFILTER)|' \
++                    -e 's|^SHOWCOORDS[ 	]*=.*$$|SHOWCOORDS=$(SHOWCOORDS)|' \
+                     "$(DESTDIR)$(bindir)/$$f" >> "$(DESTDIR)$(bindir)/$$b" \
+                 || exit 1; \
+                 ;; \

easybuild/easyconfigs/b/Blosc/Blosc-1.21.5-GCCcore-13.2.0.eb

@@ -0,0 +1,28 @@
+easyblock = 'CMakeMake'
+
+name = 'Blosc'
+version = '1.21.5'
+
+homepage = 'https://www.blosc.org/'
+
+description = "Blosc, an extremely fast, multi-threaded, meta-compressor library"
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/Blosc/c-blosc/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['32e61961bbf81ffea6ff30e9d70fca36c86178afd3e3cfa13376adec8c687509']
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('CMake', '3.27.6'),
+]
+
+sanity_check_paths = {
+    'files': ['include/blosc-export.h', 'include/blosc.h', 'lib/libblosc.a',
+              'lib/libblosc.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+moduleclass = 'lib'

easybuild/easyconfigs/b/Blosc2/Blosc2-2.13.2-GCCcore-13.2.0.eb

@@ -0,0 +1,31 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Author: Denis Kristak
+# Update: Thomas Hoffmann (EMBL)
+easyblock = 'CMakeMake'
+
+name = 'Blosc2'
+version = '2.13.2'
+
+homepage = 'https://www.blosc.org/'
+
+description = "Blosc, an extremely fast, multi-threaded, meta-compressor library"
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/Blosc/c-blosc2/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['f2adcd9615f138d1bb16dc27feadab1bb1eab01d77e5e2323d14ad4ca8c3ca21']
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('CMake', '3.27.6'),
+]
+
+sanity_check_paths = {
+    'files': ['include/blosc2/blosc2-export.h', 'include/blosc2.h', 'lib/libblosc2.a',
+              'lib/libblosc2.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+moduleclass = 'lib'

easybuild/easyconfigs/d/DIAMOND/DIAMOND-2.1.9-GCC-13.2.0.eb

@@ -0,0 +1,30 @@
+easyblock = 'CMakeMake'
+
+name = 'DIAMOND'
+version = '2.1.9'
+
+homepage = 'https://github.com/bbuchfink/diamond'
+description = "Accelerated BLAST compatible local sequence aligner"
+
+toolchain = {'name': 'GCC', 'version': '13.2.0'}
+
+github_account = 'bbuchfink'
+source_urls = [GITHUB_LOWER_SOURCE]
+sources = ['v%(version)s.tar.gz']
+checksums = ['4cde9df78c63e8aef9df1e3265cd06a93ce1b047d6dba513a1437719b70e9d88']
+
+builddependencies = [
+    ('CMake', '3.27.6'),
+]
+
+dependencies = [
+    ('zlib', '1.2.13'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/%(namelower)s'],
+    'dirs': [],
+}
+sanity_check_commands = ["%(namelower)s help"]
+
+moduleclass = 'bio'

easybuild/easyconfigs/d/denseweight/denseweight-0.1.2-foss-2022a.eb

@@ -0,0 +1,41 @@
+easyblock = 'PythonBundle'
+
+name = 'denseweight'
+version = '0.1.2'
+
+homepage = 'https://github.com/steimi/denseweight'
+description = """
+This package implements the method for imbalanced regression DenseWeight. The corresponding
+paper "Density-based weighting for imbalanced regression". The goal of DenseWeight is to allow
+training machine learning models for regression tasks that emphasize performance for data
+points with rare target values in comparison to data points with more common target values.
+"""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+    ('scikit-learn', '1.1.2'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('KDEpy', '1.1.9', {
+        'modulename': 'KDEpy',
+        'checksums': ['4bf0b2afd430ce5b40fafd98144de83d8b715d46fdf0f45fed2b5c2e9c40ce46'],
+    }),
+    (name, version, {
+        'checksums': ['281cf1fe4be364366363ee822b524620dcb629c5b9ff7852aa80f91a27c98b1e'],
+    }),
+]
+
+sanity_pip_check = True
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+moduleclass = 'ai'

easybuild/easyconfigs/g/GROMACS/GROMACS-2024.1-foss-2023b.eb

@@ -0,0 +1,87 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+#
+# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC,
+#                                 Ghent University / The Francis Crick Institute
+# Authors::
+# * Wiktor Jurkowski <[email protected]>
+# * Fotis Georgatos <[email protected]>
+# * George Tsouloupas <[email protected]>
+# * Kenneth Hoste <[email protected]>
+# * Adam Huffman <[email protected]>
+# * Ake Sandgren <[email protected]>
+# * J. Sassmannshausen <Crick HPC team>
+# * Dugan Witherick <[email protected]>
+# * Christoph Siegert <[email protected]>
+# License::   MIT/GPL
+
+name = 'GROMACS'
+version = '2024.1'
+
+homepage = 'https://www.gromacs.org'
+description = """
+GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the
+Newtonian equations of motion for systems with hundreds to millions of
+particles.
+
+This is a CPU only build, containing both MPI and threadMPI binaries
+for both single and double precision.
+
+It also contains the gmxapi extension for the single precision MPI build.
+"""
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+toolchainopts = {'openmp': True, 'usempi': True}
+
+source_urls = [
+    'https://ftp.gromacs.org/pub/gromacs/',
+    'ftp://ftp.gromacs.org/pub/gromacs/',
+]
+sources = [SOURCELOWER_TAR_GZ]
+patches = [
+    'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch',
+    'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch',
+]
+checksums = [
+    {'gromacs-2024.1.tar.gz': '937d8f12a36fffbf2af7add71adbb5aa5c5537892d46c9a76afbecab1aa0aac7'},
+    {'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch':
+     '7f41bda16c9c2837624265dda4be252f655d1288ddc4486b1a2422af30d5d199'},
+    {'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch':
+     '6df844bb3bbc51180446a3595c61a4ef195e5f975533a04cef76841aa763aec1'},
+]
+
+builddependencies = [
+    ('CMake', '3.27.6'),
+    ('scikit-build', '0.17.6'),
+]
+
+dependencies = [
+    ('Python', '3.11.5'),
+    ('SciPy-bundle', '2023.11'),
+    ('networkx', '3.2.1'),
+    ('mpi4py', '3.1.5'),
+]
+
+exts_defaultclass = 'PythonPackage'
+
+exts_default_options = {
+    'source_urls': [PYPI_SOURCE],
+    'use_pip': True,
+    'download_dep_fail': True,
+    'sanity_pip_check': True,
+}
+
+exts_list = [
+    ('gmxapi', '0.4.2', {
+        'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s ' +
+                          '-C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ',
+        'source_tmpl': 'gromacs-2023.3.tar.gz',
+        'start_dir': 'python_packaging/gmxapi',
+        'checksums': ['4ec8f8d0c7af76b13f8fd16db8e2c120e749de439ae9554d9f653f812d78d1cb'],
+    }),
+]
+
+modextrapaths = {
+    'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages',
+}
+
+moduleclass = 'bio'

easybuild/easyconfigs/h/hdWGCNA/hdWGCNA-0.3.00-foss-2023a-R-4.3.2.eb

@@ -0,0 +1,51 @@
+easyblock = 'Bundle'
+
+name = 'hdWGCNA'
+version = '0.3.00'
+versionsuffix = '-R-%(rver)s'
+local_biocver = '3.16'
+
+homepage = 'https://smorabit.github.io/hdWGCNA/'
+description = """hdWGCNA is an R package for performing weighted gene co-expression network analysis (WGCNA) in high 
+ dimensional transcriptomics data such as single-cell RNA-seq or spatial transcriptomics. hdWGCNA is highly modular 
+ and can construct context-specific co-expression networks across cellular and spatial hierarchies. hdWGNCA identifies 
+ modules of highly co-expressed genes and provides context for these modules via statistical testing and biological 
+ knowledge sources. hdWGCNA uses datasets formatted as Seurat objects."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('R', '4.3.2'),
+    ('R-bundle-CRAN', '2023.12'),
+    ('R-bundle-Bioconductor', '3.18', versionsuffix),
+]
+
+exts_defaultclass = 'RPackage'
+exts_default_options = {
+    'sources': ['%(name)s_%(version)s.tar.gz'],
+    'source_urls': [
+        'https://cran.r-project.org/src/contrib/Archive/%(name)s',  # package archive
+        'https://cran.r-project.org/src/contrib/',  # current version of packages
+        'https://cran.freestatistics.org/src/contrib',  # mirror alternative for current packages
+    ],
+}
+
+exts_list = [
+    ('tester', '0.1.7', {
+        'checksums': ['b9c645119c21c69450f3d366c911ed92ac7c14ef61652fd676a38fb9d420b5f4'],
+    }),
+    (name, version, {
+        'source_urls': ['https://github.com/smorabit/hdWGCNA/archive/'],
+        'sources': ['v%(version)s.tar.gz'],
+        'checksums': ['5ef9980f6d25b41af17ebad76722766db72fb8162d5ae7af4565893d26c9ed1f'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': [name],
+}
+
+modextrapaths = {'R_LIBS_SITE': ''}
+
+moduleclass = 'bio'

easybuild/easyconfigs/l/loompy/loompy-3.0.7-foss-2023a.eb

@@ -0,0 +1,41 @@
+easyblock = 'PythonBundle'
+
+name = 'loompy'
+version = '3.0.7'
+
+homepage = 'https://loompy.org/'
+description = "Python implementation of the Loom file format, an efficient file format for large omics datasets"
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+builddependencies = [('poetry', '1.7.1'), ]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),  # for click
+    ('SciPy-bundle', '2023.07'),
+    ('h5py', '3.9.0'),
+    ('numba', '0.58.1'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('numpy-groupies', '0.10.2', {
+        'checksums': ['f920c4ded899f5975d94fc63d634e7c89622056bbab8cc98a44d4320a0ae8a12'],
+    }),
+    (name, version, {
+        'checksums': ['b5cdf7b54734c6bed3a181d11947af70af2c6e0dcadc02fd0e871df232faa8f4'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/loompy'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ["loompy --help"]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'

easybuild/easyconfigs/m/MetaDecoder/MetaDecoder-1.0.19-foss-2023b.eb

@@ -0,0 +1,30 @@
+easyblock = 'PythonBundle'
+
+name = 'MetaDecoder'
+version = '1.0.19'
+
+homepage = 'https://github.com/liu-congcong/MetaDecoder'
+description = "An algorithm for clustering metagenomic sequences"
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+
+dependencies = [
+    ('Python', '3.11.5'),
+    ('Python-bundle-PyPI', '2023.10'),  # threadpoolctl
+    ('SciPy-bundle', '2023.11'),
+    ('scikit-learn', '1.4.0'),
+]
+
+use_pip = True
+
+exts_list = [
+    (name, version, {
+        'source_urls': ['https://github.com/liu-congcong/MetaDecoder/archive/'],
+        'sources': ['v%(version)s.tar.gz'],
+        'checksums': ['8b88813a97787bc56baa3100a576a9e56a0de02811c573573a2fffeb7e80623e'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'