Merge branch '5.0.x' into replace_parallel-5

.github/workflows/linting.yml

@@ -28,4 +28,4 @@ jobs:
       run: flake8
 
     - name: Run flake8 to verify PEP8-compliance of Easyconfigs
-      run: flake8 --select F,W605  --filename '*.eb'
+      run: flake8 --select F,W605,W291  --filename '*.eb'

easybuild/easyconfigs/a/ABRicate/ABRicate-1.0.0-gompi-2023a.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': '2023a'}
+
+# https://github.com/tseemann/abricate
+github_account = 'tseemann'
+source_urls = [GITHUB_LOWER_SOURCE]
+sources = ['v%(version)s.zip']
+checksums = ['e7e2af45e47b887c4dba754af87a24014dcb5552eb3fe2a3fd66bb5359a0daf9']
+
+dependencies = [
+    ('Perl', '5.36.1'),
+    ('any2fasta', '0.4.2'),
+    ('BioPerl', '1.7.8'),
+    ('BLAST+', '2.14.1'),
+]
+
+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/ADOL-C/ADOL-C-2.7.2-gompi-2020a.eb

@@ -9,7 +9,7 @@ description = """The package ADOL-C (Automatic Differentiation by OverLoading in
 the evaluation of first and higher derivatives of vector functions that are defined
 by computer programs written in C or C++. The resulting derivative evaluation
 routines may be called from C/C++, Fortran, or any other language that can be linked
-with C. 
+with C.
 """
 
 toolchain = {'name': 'gompi', 'version': '2020a'}

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

@@ -1,4 +1,4 @@
-# Updated to version 24.0.02 
+# Updated to version 24.0.02
 # Author: J. Sassmannshausen (Imperial College London/UK)
 
 easyblock = 'CMakeMake'

easybuild/easyconfigs/a/AMICA/AMICA-2024.1.19-intel-2023a.eb

@@ -14,7 +14,7 @@ source_urls = ['https://github.com/sccn/amica/archive/']
 sources = [{'download_filename': '%s.zip' % local_commit, 'filename': '%(name)s-%(version)s.zip'}]
 checksums = ['d856ef1bf4bd09b2aacf5da6832b9af5d7fb70976786f43585c72acd1a52443b']
 
-# original command: 
+# original command:
 # $ mpif90 -static-intel -fpp -O3 -march=core-avx2 -heap-arrays -qopenmp -mkl -DMKL -o amica17 funmod2.f90 amica17.f90
 cmds_map = [('.*', "$MPIF90 $F90FLAGS -static-intel -fpp  -heap-arrays -mkl -DMKL -o amica17 funmod2.f90 amica17.f90")]
 

easybuild/easyconfigs/a/AMRFinderPlus/AMRFinderPlus-3.12.8-gompi-2023a.eb

@@ -0,0 +1,41 @@
+easyblock = 'MakeCp'
+
+name = 'AMRFinderPlus'
+version = '3.12.8'
+
+homepage = 'https://github.com/ncbi/amr'
+description = """This software and the accompanying database are designed to find acquired antimicrobial
+ resistance genes and some point mutations in protein or assembled nucleotide sequences."""
+
+toolchain = {'name': 'gompi', 'version': '2023a'}
+
+github_account = 'ncbi'
+source_urls = ['https://github.com/ncbi/amr/archive/']
+sources = ['amrfinder_v%(version)s.tar.gz']
+checksums = ['a199bc332877bad9033a7620bc5e8e849db1f19a9ba8b7357ec5451a6a283aa0']
+
+dependencies = [
+    ('BLAST+', '2.14.1'),
+    ('HMMER', '3.4'),
+    ('cURL', '8.0.1')
+]
+
+# Binaries are installed to the root of the installation, so add that root to the PATH:
+modextrapaths = {'PATH': ''}
+
+# a list of binary files that will be produced
+local_binaries = ['amr_report', 'amrfinder', 'amrfinder_update', 'dna_mutation', 'fasta2parts', 'fasta_check',
+                  'fasta_extract', 'gff_check']
+
+files_to_copy = local_binaries
+
+sanity_check_paths = {
+    'files': local_binaries,
+    'dirs': [],
+}
+
+sanity_check_commands = [
+    ('amrfinder', '-h')
+]
+
+moduleclass = 'bio'

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

@@ -4,9 +4,9 @@ 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 
+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."""
 

easybuild/easyconfigs/a/ANIcalculator/ANIcalculator-1.0-GCCcore-11.3.0.eb

@@ -4,9 +4,9 @@ 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 
+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."""
 

easybuild/easyconfigs/a/ANSYS/ANSYS-2022R2.eb

@@ -2,8 +2,8 @@ name = 'ANSYS'
 version = '2022R2'
 
 homepage = 'https://www.ansys.com'
-description = """ANSYS simulation software enables organizations to confidently predict 
-    how their products will operate in the real world. We believe that every product is 
+description = """ANSYS simulation software enables organizations to confidently predict
+    how their products will operate in the real world. We believe that every product is
     a promise of something greater. """
 
 toolchain = SYSTEM

easybuild/easyconfigs/a/ANSYS/ANSYS-2023R1.eb

@@ -2,8 +2,8 @@ name = 'ANSYS'
 version = '2023R1'
 
 homepage = 'https://www.ansys.com'
-description = """ANSYS simulation software enables organizations to confidently predict 
-    how their products will operate in the real world. We believe that every product is 
+description = """ANSYS simulation software enables organizations to confidently predict
+    how their products will operate in the real world. We believe that every product is
     a promise of something greater. """
 
 toolchain = SYSTEM

easybuild/easyconfigs/a/AOCC/AOCC-4.2.0-GCCcore-13.3.0.eb

@@ -0,0 +1,29 @@
+name = 'AOCC'
+version = '4.2.0'
+
+homepage = 'https://developer.amd.com/amd-aocc/'
+description = """AOCC is a high-performance x86 CPU compiler for C, C++, and Fortran programming languages.
+ It supports target-dependent and target-independent optimizations. It is highly optimized for x86 targets,
+ especially for AMD “Zen”-based processors giving a performance edge for time critical HPC and other
+ applications over other compilers."""
+
+# Clang also depends on libstdc++ during runtime, but this dependency is
+# already specified as the toolchain.
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = [
+    'https://download.amd.com/developer/eula/%(namelower)s/%(namelower)s-%(version_major)s-%(version_minor)s'
+]
+sources = ['%(namelower)s-compiler-%(version)s.tar']
+checksums = ['ed5a560ec745b24dc0685ccdcbde914843fb2f2dfbfce1ba592de4ffbce1ccab']
+
+dependencies = [
+    ('binutils', '2.42'),
+    ('ncurses', '6.5'),
+    ('zlib', '1.3.1'),
+    ('libxml2', '2.12.7'),
+]
+
+clangversion = '16.0.3'
+
+moduleclass = 'compiler'

easybuild/easyconfigs/a/AOCC/AOCC-5.0.0-GCCcore-14.2.0.eb

@@ -0,0 +1,24 @@
+name = 'AOCC'
+version = '5.0.0'
+
+homepage = 'https://developer.amd.com/amd-aocc/'
+description = "AMD Optimized C/C++ & Fortran compilers (AOCC) based on LLVM 13.0"
+
+# Clang also depends on libstdc++ during runtime, but this dependency is
+# already specified as the toolchain.
+toolchain = {'name': 'GCCcore', 'version': '14.2.0'}
+
+source_urls = ['https://download.amd.com/developer/eula/aocc/aocc-5-0/']
+sources = ['aocc-compiler-%(version)s.tar']
+checksums = ['966fac2d2c759e9de6e969c10ada7a7b306c113f7f1e07ea376829ec86380daa']
+
+clangversion = '17.0.6'
+
+dependencies = [
+    ('binutils', '2.42'),
+    ('ncurses', '6.5'),
+    ('zlib', '1.3.1'),
+    ('libxml2', '2.13.4'),
+]
+
+moduleclass = 'compiler'

easybuild/easyconfigs/a/ASAP/ASAP-2.0-foss-2021a-CUDA-11.3.1.eb

@@ -5,8 +5,8 @@ version = '2.0'
 versionsuffix = '-CUDA-%(cudaver)s'
 
 homepage = "https://computationalpathologygroup.github.io/ASAP/"
-description = """ASAP focuses on fast and fluid image viewing with an easy-to-use interface 
-for making annotations. It consists of two main components: an IO library for reading and writing 
+description = """ASAP focuses on fast and fluid image viewing with an easy-to-use interface
+for making annotations. It consists of two main components: an IO library for reading and writing
 multi-resolution images and a viewer component for visualizing such images."""
 
 toolchain = {'name': 'foss', 'version': '2021a'}

easybuild/easyconfigs/a/ASAP/ASAP-2.1-foss-2022a.eb

@@ -4,8 +4,8 @@ name = 'ASAP'
 version = '2.1'
 
 homepage = 'https://computationalpathologygroup.github.io/ASAP/'
-description = """ASAP focuses on fast and fluid image viewing with an easy-to-use interface 
-for making annotations. It consists of two main components: an IO library for reading and writing 
+description = """ASAP focuses on fast and fluid image viewing with an easy-to-use interface
+for making annotations. It consists of two main components: an IO library for reading and writing
 multi-resolution images and a viewer component for visualizing such images."""
 
 toolchain = {'name': 'foss', 'version': '2022a'}

easybuild/easyconfigs/a/ATAT/ATAT-3.36-GCCcore-9.3.0.eb

@@ -6,7 +6,7 @@
 # Software, and to permit persons to whom the Software is furnished to do so, subject to the following
 # conditions:
 #
-# The above copyright notice and this permission notice shall be included in all copies or substantial portions 
+# The above copyright notice and this permission notice shall be included in all copies or substantial portions
 # of the Software.
 #
 # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED

easybuild/easyconfigs/a/ATK/ATK-2.36.0-GCCcore-10.2.0.eb

@@ -28,7 +28,7 @@ dependencies = [
     ('GLib', '2.66.1'),
 ]
 
-configopts = "--buildtype=release --default-library=both "
+configopts = "--default-library=both "
 configopts += "-Dintrospection=true "
 
 sanity_check_paths = {

easybuild/easyconfigs/a/ATK/ATK-2.36.0-GCCcore-10.3.0.eb

@@ -28,7 +28,7 @@ dependencies = [
     ('GLib', '2.68.2'),
 ]
 
-configopts = "--buildtype=release --default-library=both "
+configopts = "--default-library=both "
 configopts += "-Dintrospection=true "
 
 sanity_check_paths = {

easybuild/easyconfigs/a/ATK/ATK-2.36.0-GCCcore-11.2.0.eb

@@ -28,7 +28,7 @@ dependencies = [
     ('GLib', '2.69.1'),
 ]
 
-configopts = "--buildtype=release --default-library=both "
+configopts = "--default-library=both "
 configopts += "-Dintrospection=true "
 
 sanity_check_paths = {

easybuild/easyconfigs/a/ATK/ATK-2.36.0-GCCcore-9.3.0.eb

@@ -28,7 +28,7 @@ dependencies = [
     ('GLib', '2.64.1'),
 ]
 
-configopts = "--buildtype=release --default-library=both "
+configopts = "--default-library=both "
 configopts += "-Dintrospection=true "
 
 sanity_check_paths = {

easybuild/easyconfigs/a/ATK/ATK-2.38.0-GCCcore-11.3.0.eb

@@ -28,7 +28,7 @@ dependencies = [
     ('GLib', '2.72.1'),
 ]
 
-configopts = "--buildtype=release --default-library=both "
+configopts = "--default-library=both "
 configopts += "-Dintrospection=true "
 
 sanity_check_paths = {

easybuild/easyconfigs/a/ATK/ATK-2.38.0-GCCcore-12.2.0.eb

@@ -28,7 +28,7 @@ dependencies = [
     ('GLib', '2.75.0'),
 ]
 
-configopts = "--buildtype=release --default-library=both "
+configopts = "--default-library=both "
 configopts += "-Dintrospection=true "
 
 sanity_check_paths = {

easybuild/easyconfigs/a/ATK/ATK-2.38.0-GCCcore-12.3.0.eb

@@ -28,7 +28,7 @@ dependencies = [
     ('GLib', '2.77.1'),
 ]
 
-configopts = "--buildtype=release --default-library=both "
+configopts = "--default-library=both "
 configopts += "-Dintrospection=true "
 
 sanity_check_paths = {

easybuild/easyconfigs/a/ATK/ATK-2.38.0-GCCcore-13.2.0.eb

@@ -28,7 +28,7 @@ dependencies = [
     ('GLib', '2.78.1'),
 ]
 
-configopts = "--buildtype=release --default-library=both "
+configopts = "--default-library=both "
 configopts += "-Dintrospection=true "
 
 sanity_check_paths = {

easybuild/easyconfigs/a/ATK/ATK-2.38.0-GCCcore-13.3.0.eb

@@ -28,7 +28,7 @@ dependencies = [
     ('GLib', '2.80.4'),
 ]
 
-configopts = "--buildtype=release --default-library=both "
+configopts = "--default-library=both "
 configopts += "-Dintrospection=true "
 
 sanity_check_paths = {