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

…asyconfigs into 20211108232530_new_pr_pangolin3116

easybuild/easyconfigs/a/ABINIT/ABINIT-9.4.2-foss-2021a.eb

@@ -0,0 +1,65 @@
+easyblock = 'ConfigureMake'
+
+name = 'ABINIT'
+version = '9.4.2'
+
+homepage = 'https://www.abinit.org/'
+description = """ABINIT is a package whose main program allows one to find the total energy,
+  charge density and electronic structure of systems made of electrons and nuclei (molecules
+  and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a
+  planewave or wavelet basis."""
+
+toolchain = {'name': 'foss', 'version': '2021a'}
+toolchainopts = {'usempi': True, 'pic': True}
+
+source_urls = ['https://www.abinit.org/sites/default/files/packages/']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['d40886f5c8b138bb4aa1ca05da23388eb70a682790cfe5020ecce4db1b1a76bc']
+
+builddependencies = [
+    ('Python', '3.9.5'),
+]
+dependencies = [
+    ('libxc', '5.1.5'),
+    ('netCDF', '4.8.0'),
+    ('netCDF-Fortran', '4.5.3'),
+    ('HDF5', '1.10.7'),
+    ('Wannier90', '3.1.0'),
+]
+
+# Needed due to changes in GCC10.
+configopts = 'FCFLAGS="-fallow-argument-mismatch -ffree-line-length-none $FCFLAGS" '
+configopts += 'FFLAGS="-fallow-argument-mismatch $FFLAGS" '
+
+# Ensure MPI
+configopts += '--with-mpi="yes" --enable-openmp="no" '
+# configopts += ' FC="mpiifort" CC="mpiicc" CXX="mpiicpc" '
+
+# BLAS/Lapack from OpenBLAS
+configopts += '--with-linalg-flavor="openblas"  LINALG_LIBS="${LIBLAPACK_MT}" '
+
+# FFTW
+configopts += '--with-fft-flavor=fftw3 FFTW3_LIBS="-L${EBROOTFFTW} -lfftw3f -lfftw3" '
+
+# libxc support
+configopts += '--with-libxc=${EBROOTLIBXC} '
+
+# hdf5/netcdf4 support
+configopts += '--with-netcdf="${EBROOTNETCDF}" '
+configopts += '--with-netcdf-fortran="${EBROOTNETCDFMINFORTRAN}" '
+configopts += '--with-hdf5="${EBROOTHDF5}" '
+
+# Wannier90
+configopts += '--with-wannier90="${EBROOTWANNIER90}" '
+preconfigopts = 'export WANNIER90_LIBS="-L$EBROOTWANNIER90/lib -lwannier" && '
+
+# 'make check' is just executing some basic unit tests.
+# Also running 'make tests_v1' to have some basic validation
+runtest = "check && make test_v1"
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']],
+    'dirs': ['lib/pkgconfig'],
+}
+
+moduleclass = 'chem'

easybuild/easyconfigs/a/ABINIT/ABINIT-9.6.2-intel-2021a.eb

@@ -0,0 +1,68 @@
+easyblock = 'ConfigureMake'
+
+name = 'ABINIT'
+version = '9.6.2'
+
+homepage = 'https://www.abinit.org/'
+description = """
+ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of
+systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using
+pseudopotentials and a planewave or wavelet basis.
+"""
+
+toolchain = {'name': 'intel', 'version': '2021a'}
+toolchainopts = {'usempi': True, 'openmp': True, 'pic': True}
+
+source_urls = ['https://www.abinit.org/sites/default/files/packages/']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['b018c2ff24338a5952c5550a7e09d4c7793b62402c7aa4e09273e9a666e674fb']
+
+builddependencies = [
+    ('Python', '3.9.5'),
+]
+dependencies = [
+    ('libxc', '5.1.5'),
+    ('netCDF', '4.8.0'),
+    ('netCDF-Fortran', '4.5.3'),
+    ('HDF5', '1.10.7'),
+    ('Wannier90', '3.1.0'),
+]
+
+# Ensure MPI with intel wrappers.
+configopts = '--with-mpi="yes" '
+configopts += ' FC="mpiifort" CC="mpiicc" CXX="mpiicpc" '
+
+# Enable OpenMP
+configopts += '--enable-openmp="yes" '
+
+# BLAS/Lapack from MKL
+configopts += '--with-linalg-flavor=mkl '
+
+# FFTW from MKL
+configopts += '--with-fft-flavor=dfti '
+
+# libxc support
+configopts += '--with-libxc=${EBROOTLIBXC} '
+
+# hdf5/netcdf4 support
+configopts += '--with-netcdf="${EBROOTNETCDF}" '
+configopts += '--with-netcdf-fortran="${EBROOTNETCDFMINFORTRAN}" '
+configopts += '--with-hdf5="${EBROOTHDF5}" '
+
+# Wannier90
+configopts += '--with-wannier90="${EBROOTWANNIER90}" '
+preconfigopts = 'export WANNIER90_LIBS="-L$EBROOTWANNIER90/lib -lwannier" && '
+
+# Enable double precision for GW calculations
+configopts += '--enable-gw-dpc '
+
+# 'make check' is just executing some basic unit tests.
+# Also running 'make tests_v1' to have some basic validation
+runtest = "check && make test_v1"
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']],
+    'dirs': ['lib/pkgconfig'],
+}
+
+moduleclass = 'chem'

easybuild/easyconfigs/a/ABINIT/ABINIT-9.6.2-intel-2021b.eb

@@ -0,0 +1,71 @@
+easyblock = 'ConfigureMake'
+
+name = 'ABINIT'
+version = '9.6.2'
+
+homepage = 'https://www.abinit.org/'
+description = """
+ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of
+systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using
+pseudopotentials and a planewave or wavelet basis.
+"""
+
+toolchain = {'name': 'intel', 'version': '2021b'}
+toolchainopts = {'usempi': True, 'openmp': True, 'pic': True}
+
+source_urls = ['https://www.abinit.org/sites/default/files/packages/']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['b018c2ff24338a5952c5550a7e09d4c7793b62402c7aa4e09273e9a666e674fb']
+
+builddependencies = [
+    ('Python', '3.9.6'),
+]
+dependencies = [
+    ('libxc', '5.1.6'),
+    ('netCDF', '4.8.1'),
+    ('netCDF-Fortran', '4.5.3'),
+    ('HDF5', '1.12.1'),
+    ('Wannier90', '3.1.0'),
+]
+
+# Ensure MPI with intel wrappers.
+configopts = '--with-mpi="yes" '
+configopts += ' FC="mpiifort" CC="mpiicc" CXX="mpiicpc" '
+
+# Enable OpenMP
+configopts += '--enable-openmp="yes" '
+
+# BLAS/Lapack from MKL
+configopts += '--with-linalg-flavor=mkl '
+
+# FFTW from MKL
+configopts += '--with-fft-flavor=dfti '
+
+# libxc support
+configopts += '--with-libxc=${EBROOTLIBXC} '
+
+# hdf5/netcdf4 support
+configopts += '--with-netcdf="${EBROOTNETCDF}" '
+configopts += '--with-netcdf-fortran="${EBROOTNETCDFMINFORTRAN}" '
+configopts += '--with-hdf5="${EBROOTHDF5}" '
+
+# Wannier90
+configopts += '--with-wannier90="${EBROOTWANNIER90}" '
+preconfigopts = 'export WANNIER90_LIBS="-L$EBROOTWANNIER90/lib -lwannier" && '
+
+# Enable double precision for GW calculations
+configopts += '--enable-gw-dpc '
+
+# Enable OpenMP
+configopts += '--enable-openmp '
+
+# 'make check' is just executing some basic unit tests.
+# Also running 'make tests_v1' to have some basic validation
+runtest = "check && make test_v1"
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']],
+    'dirs': ['lib/pkgconfig'],
+}
+
+moduleclass = 'chem'

easybuild/easyconfigs/a/ABRicate/ABRicate-1.0.0-gompi-2021a.eb

@@ -0,0 +1,41 @@
+# Author: Pavel Grochal (INUITS)
+# License: GPLv2
+
+easyblock = 'Tarball'
+
+name = 'ABRicate'
+version = '1.0.0'
+
+homepage = 'https://github.com/tseemann/abricate'
+description = "Mass screening of contigs for antimicrobial and virulence genes"
+
+toolchain = {'name': 'gompi', 'version': '2021a'}
+
+# https://github.com/tseemann/abricate
+github_account = 'tseemann'
+source_urls = [GITHUB_LOWER_SOURCE]
+sources = ['v%(version)s.zip']
+checksums = ['e7e2af45e47b887c4dba754af87a24014dcb5552eb3fe2a3fd66bb5359a0daf9']
+
+dependencies = [
+    ('Perl', '5.32.1'),
+    ('any2fasta', '0.4.2'),
+    ('BioPerl', '1.7.8'),
+    ('BLAST+', '2.11.0'),
+]
+
+postinstallcmds = ['%(installdir)s/bin/abricate --setupdb']
+
+sanity_check_paths = {
+    'files': ['bin/abricate', 'bin/abricate-get_db'],
+    'dirs': ['db'],
+}
+
+sanity_check_commands = [
+    "abricate --help",
+    "abricate --list",
+]
+
+modloadmsg = "abricate databases are located in $EBROOTABRICATE/db\n"
+
+moduleclass = 'bio'

easybuild/easyconfigs/a/ANIcalculator/ANIcalculator-1.0-GCCcore-10.3.0.eb

@@ -0,0 +1,45 @@
+# This installation only works for Linux distributions that provide libnsl.so.1 as part of the (g)libc package.
+easyblock = 'MakeCp'
+
+name = 'ANIcalculator'
+version = '1.0'
+
+homepage = 'https://ani.jgi.doe.gov/html/home.php'
+description = """This tool will calculate the bidirectional average nucleotide identity (gANI) and 
+Alignment Fraction (AF) between two genomes. Required input is the full path to the fna file 
+(nucleotide sequence of genes in fasta format) of each query genome. Either the rRNA and tRNA genes 
+can be excluded, or provided in a list with the -ignoreList option. This is necessary as the presence
+of tRNA and/or rRNA genes in the fna will artificially inflate the ANI."""
+
+toolchain = {'name': 'GCCcore', 'version': '10.3.0'}
+
+source_urls = ['https://ani.jgi.doe.gov/download_files/']
+sources = ['%(name)s_v%(version_major)s.tgz']
+checksums = ['236596a9a204cbcad162fc66be3506b2530b1f48f4f84d9647ccec3ca7483a43']
+
+builddependencies = [('binutils', '2.36.1')]
+
+dependencies = [
+    ('Perl', '5.32.1'),
+]
+
+skipsteps = ['build']
+
+# The source tarball also includes Log4perl 1.44.
+# Instead of copying this, we use the version from the Perl module.
+files_to_copy = [(['ANIcalculator', 'nsimscan'], 'bin'), 'README.txt']
+
+# Remove the execute permissions on the README.txt, which it has by default.
+postinstallcmds = ['chmod -x %(installdir)s/README.txt']
+
+sanity_check_paths = {
+    'files': ['README.txt', 'bin/ANIcalculator', 'bin/nsimscan'],
+    'dirs': [],
+}
+
+sanity_check_commands = [
+    'ANIcalculator -help',
+    'nsimscan -h',
+]
+
+moduleclass = 'bio'

easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-11.2.0-Java-11.eb

@@ -0,0 +1,36 @@
+easyblock = 'ConfigureMake'
+
+name = 'ANTLR'
+version = '2.7.7'
+versionsuffix = '-Java-%(javaver)s'
+
+homepage = 'https://www.antlr2.org/'
+description = """ANTLR, ANother Tool for Language Recognition, (formerly PCCTS)
+ is a language tool that provides a framework for constructing recognizers,
+ compilers, and translators from grammatical descriptions containing
+ Java, C#, C++, or Python actions."""
+
+toolchain = {'name': 'GCCcore', 'version': '11.2.0'}
+
+source_urls = ['https://www.antlr2.org/download/']
+sources = [SOURCELOWER_TAR_GZ]
+patches = ['%(name)s-%(version)s_includes.patch']
+checksums = [
+    '853aeb021aef7586bda29e74a6b03006bcb565a755c86b66032d8ec31b67dbb9',  # antlr-2.7.7.tar.gz
+    'd167d3248a03301bc93efcb37d5df959aae6794968e42231af0b0dd26d6a2e66',  # ANTLR-2.7.7_includes.patch
+]
+
+builddependencies = [('binutils', '2.37')]
+
+dependencies = [('Java', '11', '', True)]
+
+configopts = '--disable-examples --disable-csharp --disable-python'
+
+sanity_check_paths = {
+    'files': ['bin/antlr', 'bin/antlr-config'],
+    'dirs': ['include'],
+}
+
+sanity_check_commands = ["antlr --help"]
+
+moduleclass = 'tools'

easybuild/easyconfigs/a/ARAGORN/ARAGORN-1.2.41-foss-2021b.eb

@@ -0,0 +1,44 @@
+# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/
+# Author: Pablo Escobar Lopez
+# sciCORE - University of Basel
+# SIB Swiss Institute of Bioinformatics
+# Updated: Denis Kristak
+
+easyblock = 'CmdCp'
+
+name = 'ARAGORN'
+version = '1.2.41'
+
+homepage = 'http://www.ansikte.se/ARAGORN/'
+description = "a program to detect tRNA genes and tmRNA genes in nucleotide sequences"
+
+toolchain = {'name': 'foss', 'version': '2021b'}
+
+source_urls = ['http://www.ansikte.se/ARAGORN/Downloads/']
+sources = [
+    {'filename': '%(namelower)s%(version)s.c', 'extract_cmd': 'cp %s aragorn.c'},
+    {'download_filename': 'aragorn.1', 'filename': 'aragorn-%(version)s.man', 'extract_cmd': 'cp %s aragorn.1'}
+]
+checksums = [
+    '92a31cc5c0b0ad16d4d7b01991989b775f07d2815df135fe6e3eab88f5e97f4a',  # aragorn1.2.41.c
+    '6e30f6d9da644197064744f033176969e77855964ed8d50ea00c38a3aea2c92e',  # aragorn.1
+]
+
+cmds_map = [
+    (".*.c", "$CC $CFLAGS -o aragorn aragorn.c"),
+    (".*.1", "mkdir -p share/man/man1 && cp aragorn.1 share/man/man1"),  # mapping command to manpage srcfile
+]
+
+files_to_copy = [
+    (['aragorn'], 'bin'),
+    'share',
+]
+
+sanity_check_paths = {
+    'files': ['bin/aragorn'],
+    'dirs': ['share/man'],
+}
+
+sanity_check_commands = ['aragorn --help']
+
+moduleclass = 'bio'