Merge pull request #20314 from boegel/5.0.x

sync with develop (20240406)

easybuild/easyconfigs/a/AFNI/AFNI-24.0.02-foss-2023a.eb

@@ -0,0 +1,67 @@
+# Updated to version 24.0.02 
+# Author: J. Sassmannshausen (Imperial College London/UK)
+
+easyblock = 'CMakeMake'
+
+name = 'AFNI'
+version = '24.0.02'
+
+homepage = 'http://afni.nimh.nih.gov/'
+description = """AFNI is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data -
+ a technique for mapping human brain activity."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+toolchainopts = {'openmp': True, 'pic': True}
+
+source_urls = ['https://github.com/afni/afni/archive/']
+sources = ['AFNI_%(version)s.tar.gz']
+checksums = ['2915ed5bf98712abe3373bfc285f946fdee6cf1367e23ba80575dd6eedb3529a']
+
+builddependencies = [
+    ('CMake', '3.26.3'),
+]
+
+dependencies = [
+    ('tcsh', '6.24.10'),
+    ('Python', '3.11.3'),
+    ('X11', '20230603'),
+    ('motif', '2.3.8'),
+    ('R', '4.3.2'),
+    ('PyQt5', '5.15.10'),
+    ('expat', '2.5.0'),
+    ('libpng', '1.6.39'),
+    ('libjpeg-turbo', '2.1.5.1'),
+    ('GSL', '2.7'),
+    ('GLib', '2.77.1'),
+    ('zlib', '1.2.13'),
+    ('freeglut', '3.4.0'),
+    ('Pillow', '10.0.0'),
+    ('matplotlib', '3.7.2'),
+    ('SciPy-bundle', '2023.07'),
+    ('Xvfb', '21.1.8'),
+    ('FFmpeg', '6.0'),  # required for running the program
+]
+
+# Make sure stuff does not get installed in .local
+configopts = '-DSTANDARD_PYTHON_INSTALL=OFF '
+
+# Changing permissions of some files
+postinstallcmds = ['chmod a+x %(installdir)s/bin/afni_system_check.py ;']
+postinstallcmds += ['chmod a+x %(installdir)s/bin/uber_subject.py ; ']
+postinstallcmds += ['chmod a+x %(installdir)s/bin/init_user_dotfiles.py ; ']
+# Copying apparently missing files over
+postinstallcmds += ['cp -f %(start_dir)s/src/discoraj/ClusterExplorer/ClustExp_HistTable.py %(installdir)s/bin ; ']
+postinstallcmds += ['cp -f %(start_dir)s/src/discoraj/ClusterExplorer/ClustExp_StatParse.py %(installdir)s/bin ; ']
+postinstallcmds += ['cp -rf %(start_dir)s/src/scripts_for_r %(installdir)s/bin ; ']
+postinstallcmds += ['cp -rf %(start_dir)s/src/R_scripts %(installdir)s/bin/scripts_for_r ; ']
+
+sanity_check_commands = ["afni -help"]
+
+sanity_check_paths = {
+    'files': ['bin/afni', 'lib/libgts.%s' % SHLIB_EXT, 'lib/libnifti2.%s' % SHLIB_EXT],
+    'dirs': ['include', 'share'],
+}
+
+modextrapaths = {'PATH': ['bin/scripts_for_r']}
+
+moduleclass = 'bio'

easybuild/easyconfigs/a/AreTomo2/AreTomo2-1.0.0-GCCcore-12.3.0-CUDA-12.1.1.eb

@@ -0,0 +1,55 @@
+# Thomas Hoffmann, EMBL Heidelberg, [email protected], 2024/1
+easyblock = 'MakeCp'
+
+name = 'AreTomo2'
+version = '1.0.0'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://github.com/czimaginginstitute/AreTomo2'
+
+description = """AreTomo2, a multi-GPU accelerated software package that fully automates motion- 
+corrected marker-free tomographic alignment and reconstruction, now includes    
+robust GPU-accelerated CTF (Contrast Transfer Function) estimation in a single  
+package. AreTomo2 is part of our endeavor to build a fully-automated high-      
+throughput processing pipeline that enables real-time reconstruction of         
+tomograms in parallel with tomographic data collection. It strives to be fast   
+and accurate, as well as provides for easy integration into subtomogram         
+processing workflows by generating IMod compatible files containing alignment   
+and CTF parameters needed to bootstrap subtomogram averaging. AreTomo2 can also 
+be used for on-the-fly reconstruction of tomograms and CTF estimation in        
+parallel with tilt series collection, enabling real-time assessment of sample   
+quality and adjustment of collection parameters"""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchainopts = {'cstd': 'c++11'}
+
+source_urls = [GITHUB_SOURCE]
+sources = ['v%(version)s.tar.gz']
+patches = ['%(name)s-%(version)s_makefile.patch']
+checksums = [
+    {'v1.0.0.tar.gz': '5518cd5d7bc13a6dbb6d9310b22c301e73a0c91dc059da403445d79ca0ff8892'},
+    {'AreTomo2-1.0.0_makefile.patch': '8595b2fc55e0b5e1bf7c077c93c09503b4e8f95123c6aaf0a5fbe44dda871c73'},
+]
+
+github_account = 'czimaginginstitute'
+
+build_cmd = 'make exe -f makefile11 CUDAHOME=$CUDA_HOME CUDACC="%(cuda_cc_cmake)s"'
+
+builddependencies = [
+    ('binutils', '2.40')
+]
+
+dependencies = [
+    ('CUDA', '12.1.1', '', SYSTEM),
+]
+
+files_to_copy = [(['%(name)s'], 'bin')]
+
+sanity_check_paths = {
+    'files': ['bin/%(name)s'],
+    'dirs': ['bin'],
+}
+
+sanity_check_commands = ['%(name)s -h']
+
+moduleclass = 'bio'

easybuild/easyconfigs/a/AreTomo2/AreTomo2-1.0.0_makefile.patch

@@ -0,0 +1,46 @@
+# Thomas Hoffmann, EBML Heidelberg, [email protected], 2023/10
+# allow to inject cuda compute capabilities and cfalgs
+diff -ru AreTomo2-1.0.0/makefile11 AreTomo2-1.0.0_makefile/makefile11
+--- AreTomo2-1.0.0/makefile11	2023-10-26 19:49:07.000000000 +0200
++++ AreTomo2-1.0.0_makefile/makefile11	2023-10-30 19:00:07.212270395 +0100
+@@ -156,18 +156,21 @@
+ 	$(CUCPPS)
+ OBJS = $(patsubst %.cpp, %.o, $(SRCS))
+ #-------------------------------------
+-CC = g++ -std=c++11
+-CFLAG = -c -g -pthread -m64
++#CC = g++ -std=c++11
++CFLAG = -c -g -pthread -m64 $(CFLAGS)
+ NVCC = $(CUDAHOME)/bin/nvcc -std=c++11
+-CUFLAG = -Xptxas -dlcm=ca -O2 \
+-	-gencode arch=compute_80,code=sm_80 \
+-	-gencode arch=compute_75,code=sm_75 \
+-	-gencode arch=compute_70,code=sm_70 \
+-	-gencode arch=compute_61,code=sm_61 \
+-	-gencode arch=compute_60,code=sm_60 \
+-	-gencode arch=compute_53,code=sm_53 \
+-	-gencode arch=compute_52,code=sm_52 \
+-	-gencode arch=compute_86,code=sm_86
++SPACE= ' '
++SEMI= ;
++GENCODES = $(foreach x,$(subst $(SEMI),$(SPACE),$(CUDACC)),-gencode arch=compute_$x,code=sm_$x)
++CUFLAG = -Xptxas -dlcm=ca -O2 $(GENCODES)
++#	-gencode arch=compute_80,code=sm_80 \
++#	-gencode arch=compute_75,code=sm_75 \
++#	-gencode arch=compute_70,code=sm_70 \
++#	-gencode arch=compute_61,code=sm_61 \
++#	-gencode arch=compute_60,code=sm_60 \
++#	-gencode arch=compute_53,code=sm_53 \
++#	-gencode arch=compute_52,code=sm_52 \
++#	-gencode arch=compute_86,code=sm_86
+ #------------------------------------------
+ cuda: $(CUCPPS)
+
+@@ -183,6 +186,7 @@
+ 	-lcufft -lcudart -lcuda -lc -lm -lpthread \
+ 	-o AreTomo2
+ 	@echo AreTomo2 has been generated.
++	@echo used cuda gencodes: $(GENCODES)
+
+ %.o: %.cu
+ 	@$(NVCC) -c $(CUFLAG) -I$(PRJINC) -I$(CUPRJINC) $< -o $@

easybuild/easyconfigs/a/ant/ant-1.10.14-Java-21.eb

@@ -0,0 +1,27 @@
+easyblock = 'PackedBinary'
+
+name = 'ant'
+version = '1.10.14'
+versionsuffix = '-Java-%(javaver)s'
+
+homepage = 'https://ant.apache.org/'
+description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in
+ build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of
+ Java applications."""
+
+toolchain = SYSTEM
+
+source_urls = ['https://archive.apache.org/dist/ant/binaries/']
+sources = ['apache-%(name)s-%(version)s-bin.tar.gz']
+checksums = ['e2852fddaaddc1ab76a099ca0d7b2ee47a907b8a91a64f70f6aa9e6a3d0dd504']
+
+dependencies = [('Java', '21')]
+
+sanity_check_paths = {
+    'files': ['bin/ant', 'lib/ant.jar'],
+    'dirs': [],
+}
+
+modextravars = {'ANT_HOME': '%(installdir)s'}
+
+moduleclass = 'devel'

easybuild/easyconfigs/a/argtable/argtable-2.13-GCCcore-11.2.0.eb

@@ -0,0 +1,30 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Author: Pablo Escobar Lopez
+# Swiss Institute of Bioinformatics
+# Biozentrum - University of Basel
+# Modified by: Adam Huffman
+# The Francis Crick Institute
+
+easyblock = 'ConfigureMake'
+
+name = 'argtable'
+version = '2.13'
+
+homepage = 'https://argtable.sourceforge.io/'
+description = """ Argtable is an ANSI C library for parsing GNU style
+ command line options with a minimum of fuss. """
+
+toolchain = {'name': 'GCCcore', 'version': '11.2.0'}
+
+source_urls = [SOURCEFORGE_SOURCE]
+sources = ['%s%s.tar.gz' % (name, version.replace('.', '-'))]
+checksums = ['8f77e8a7ced5301af6e22f47302fdbc3b1ff41f2b83c43c77ae5ca041771ddbf']
+
+builddependencies = [('binutils', '2.37')]
+
+sanity_check_paths = {
+    'files': ['include/argtable2.h', 'lib/libargtable2.%s' % SHLIB_EXT, 'lib/libargtable2.a'],
+    'dirs': ['share'],
+}
+
+moduleclass = 'lib'

easybuild/easyconfigs/a/assimp/assimp-5.3.1-GCCcore-13.2.0.eb

@@ -0,0 +1,36 @@
+# Authors:: Richard Lawrence  <[email protected]> - TAMU HPRC - https://hprc.tamu.edu
+
+easyblock = 'CMakeMake'
+
+name = 'assimp'
+version = '5.3.1'
+
+homepage = 'https://github.com/assimp/assimp'
+
+description = """
+ Open Asset Import Library (assimp) is a library to import and export various
+ 3d-model-formats including scene-post-processing to generate missing render data.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
+source_urls = ['https://github.com/%(name)s/%(name)s/archive']
+sources = ['v%(version)s.tar.gz']
+checksums = ['a07666be71afe1ad4bc008c2336b7c688aca391271188eb9108d0c6db1be53f1']
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('pkgconf', '2.0.3'),
+    ('CMake', '3.27.6'),
+    ('zlib', '1.2.13'),
+]
+
+# workaround bug with GCC13 https://github.com/assimp/assimp/issues/5315
+configopts = '-DASSIMP_WARNINGS_AS_ERRORS=OFF '
+
+sanity_check_paths = {
+    'files': ['include/assimp/types.h', 'lib/libassimp.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+moduleclass = 'vis'

easybuild/easyconfigs/b/biom-format/biom-format-2.1.15-foss-2023a.eb

@@ -0,0 +1,44 @@
+##
+# 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::     Revised BSD
+#
+# Notes:: updated by Kenneth Hoste (HPC-UGent) for foss/2021b
+##
+# Updated: Petr Král (INUITS)
+
+easyblock = 'PythonPackage'
+
+name = 'biom-format'
+version = '2.1.15'
+
+homepage = 'https://biom-format.org'
+description = """
+The BIOM file format (canonically pronounced biome) is designed to be
+ a general-use format for representing biological sample by observation
+ contingency tables. BIOM is a recognized standard for the Earth Microbiome
+ Project and is a Genomics Standards Consortium supported project.
+"""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+toolchainopts = {'usempi': True}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['3bda2096e663dc1cb6f90f51b394da0838b9be5164a44370c134ce5b3b2a4dd3']
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('h5py', '3.9.0'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/biom'],
+    'dirs': ['lib'],
+}
+
+options = {'modulename': 'biom'}
+
+moduleclass = 'bio'

easybuild/easyconfigs/c/Clustal-Omega/Clustal-Omega-1.2.4-GCC-11.2.0.eb

@@ -0,0 +1,35 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Author: Pablo Escobar Lopez
+# Swiss Institute of Bioinformatics
+# Biozentrum - University of Basel
+# Modified by Adam Huffman
+# Francis Crick Institute
+
+easyblock = 'ConfigureMake'
+
+name = 'Clustal-Omega'
+version = '1.2.4'
+
+homepage = 'http://www.clustal.org/omega/'
+description = """ Clustal Omega is a multiple sequence alignment
+ program for proteins. It produces biologically meaningful multiple
+ sequence alignments of divergent sequences. Evolutionary relationships
+ can be seen via viewing Cladograms or Phylograms """
+
+toolchain = {'name': 'GCC', 'version': '11.2.0'}
+toolchainopts = {'openmp': True}
+
+source_urls = [homepage]
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['8683d2286d663a46412c12a0c789e755e7fd77088fb3bc0342bb71667f05a3ee']
+
+dependencies = [('argtable', '2.13')]
+
+sanity_check_paths = {
+    'files': ['bin/clustalo'],
+    'dirs': [],
+}
+
+sanity_check_commands = ["clustalo --help"]
+
+moduleclass = 'bio'

easybuild/easyconfigs/c/contextily/contextily-1.5.0-foss-2023a.eb

@@ -0,0 +1,35 @@
+easyblock = 'PythonBundle'
+
+name = 'contextily'
+version = '1.5.0'
+
+homepage = 'https://contextily.readthedocs.io/'
+description = """contextily is a small Python 3 package to retrieve tile maps from the internet.
+It can add those tiles as basemap to matplotlib figures or write tile maps to
+disk into geospatial raster files. Bounding boxes can be passed in both WGS84
+(EPSG:4326) and Spheric Mercator (EPSG:3857)."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('geopy', '2.4.1'),
+    ('matplotlib', '3.7.2'),
+    ('Pillow', '10.0.0'),
+    ('rasterio', '1.3.9'),
+]
+
+exts_list = [
+    ('xyzservices', '2023.7.0', {
+        'checksums': ['0ec928742227d6f5d4367ea7b457fcfed943429f4de2949b5b02a82cdf5569d6'],
+    }),
+    ('mercantile', '1.2.1', {
+        'checksums': ['fa3c6db15daffd58454ac198b31887519a19caccee3f9d63d17ae7ff61b3b56b'],
+    }),
+    (name, version, {
+        'checksums': ['295b2d8097f8f6e80e1cb5e6e77538d1cdf729f827ec54eedc57f613c0a3ce0e'],
+    }),
+]
+
+moduleclass = 'geo'