diff --git a/easybuild/easyblocks/p/pasha.py b/easybuild/easyblocks/p/pasha.py deleted file mode 100644 index 9634aad21f..0000000000 --- a/easybuild/easyblocks/p/pasha.py +++ /dev/null @@ -1,68 +0,0 @@ -## -# Copyright 2009-2024 Ghent University -# -# This file is part of EasyBuild, -# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en), -# with support of Ghent University (http://ugent.be/hpc), -# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be), -# Flemish Research Foundation (FWO) (http://www.fwo.be/en) -# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en). -# -# https://github.com/easybuilders/easybuild -# -# EasyBuild is free software: you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation v2. -# -# EasyBuild is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. -# -# You should have received a copy of the GNU General Public License -# along with EasyBuild. If not, see . -## -""" -EasyBuild support for building and installing Pasha, implemented as an easyblock - -@author: Jens Timmerman (Ghent University) -""" - -import shutil -import os - -from easybuild.easyblocks.generic.configuremake import ConfigureMake -from easybuild.tools.build_log import EasyBuildError -from easybuild.tools.modules import get_software_root - - -class EB_Pasha(ConfigureMake): - """Support for building and installing Pasha""" - - def configure_step(self): - """Configure Pasha by setting make options.""" - - tbb = get_software_root('TBB') - if not tbb: - raise EasyBuildError("TBB module not loaded.") - - self.cfg.update('buildopts', "TBB_DIR=%s/tbb MPI_DIR='' MPI_INC='' " % tbb) - self.cfg.update('buildopts', 'MPI_CXX="%s"' % os.getenv('MPICXX')) - self.cfg.update('buildopts', 'OPM_FLAG="%s"' % self.toolchain.get_flag('openmp')) - self.cfg.update('buildopts', 'MPI_LIB="" MY_CXX="%s" MPICH_IGNORE_CXX_SEEK=1' % os.getenv('CXX')) - - def install_step(self): - """Install by copying everything from 'bin' subdir in build dir to install dir""" - - srcdir = os.path.join(self.builddir, "%s-%s" % (self.name, self.version), 'bin') - shutil.copytree(srcdir, os.path.join(self.installdir, 'bin')) - - def sanity_check_step(self): - """Custom sanity check for Pasha""" - - custom_paths = { - 'files': ["bin/pasha-%s" % x for x in ["kmergen", "pregraph", "graph"]], - 'dirs': [], - } - - super(EB_Pasha, self).sanity_check_step(custom_paths=custom_paths) diff --git a/easybuild/easyblocks/p/pbdmpi.py b/easybuild/easyblocks/p/pbdmpi.py deleted file mode 100644 index 1c7310d29f..0000000000 --- a/easybuild/easyblocks/p/pbdmpi.py +++ /dev/null @@ -1,59 +0,0 @@ -## -# Copyright 2015-2024 Ghent University -# -# This file is part of EasyBuild, -# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en), -# with support of Ghent University (http://ugent.be/hpc), -# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be), -# Flemish Research Foundation (FWO) (http://www.fwo.be/en) -# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en). -# -# https://github.com/easybuilders/easybuild -# -# EasyBuild is free software: you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation v2. -# -# EasyBuild is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. -# -# You should have received a copy of the GNU General Public License -# along with EasyBuild. If not, see . -## -""" -EasyBuild support for building and installing pbdMPI, implemented as an easyblock - -@author: Ewan Higgs (Ghent University) -@author: Peter Maxwell (University of Auckland) -""" - -import easybuild.tools.toolchain as toolchain -from easybuild.easyblocks.generic.rpackage import RPackage - - -class EB_pbdMPI(RPackage): - """Support for building/installing pbdMPI.""" - - def configure_step(self): - """Configure Step of build process for pbdMPI.""" - mpi_types = { - toolchain.INTELMPI: 'INTELMPI', - toolchain.MPI_TYPE_MPICH: 'MPICH', - toolchain.MPI_TYPE_OPENMPI: 'OPENMPI', - } - mpi_type = mpi_types[self.toolchain.mpi_family()] - self.configureargs.extend([ - "--with-mpi-include=%s" % self.toolchain.get_variable('MPI_INC_DIR'), - "--with-mpi-libpath=%s" % self.toolchain.get_variable('MPI_LIB_DIR'), - "--with-mpi=%s" % self.toolchain.get_software_root(self.toolchain.MPI_MODULE_NAME)[0], - "--with-mpi-type=%s" % mpi_type, - ]) - - super(EB_pbdMPI, self).configure_step() - - def install_extension(self): - """Configure before installing pbdMPI as an extension.""" - self.configure_step() - super(EB_pbdMPI, self).install_extension() diff --git a/easybuild/easyblocks/p/pbdslap.py b/easybuild/easyblocks/p/pbdslap.py deleted file mode 100644 index 1337c02f60..0000000000 --- a/easybuild/easyblocks/p/pbdslap.py +++ /dev/null @@ -1,40 +0,0 @@ -## -# Copyright 2015-2024 Ghent University -# -# This file is part of EasyBuild, -# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en), -# with support of Ghent University (http://ugent.be/hpc), -# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be), -# Flemish Research Foundation (FWO) (http://www.fwo.be/en) -# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en). -# -# https://github.com/easybuilders/easybuild -# -# EasyBuild is free software: you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation v2. -# -# EasyBuild is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. -# -# You should have received a copy of the GNU General Public License -# along with EasyBuild. If not, see . -## -""" -EasyBuild support for building and installing pbdSLAP, implemented as an easyblock - -@author: Ewan Higgs (Ghent University) -""" - -from easybuild.easyblocks.generic.rpackage import RPackage - - -class EB_pbdSLAP(RPackage): - """Support for building/installing pbdSLAP.""" - - def __init__(self, *args, **kwargs): - """Initialisation of custom class variables for pbdSLAP.""" - super(EB_pbdSLAP, self).__init__(*args, **kwargs) - self.configurevars.append("EXT_LDFLAGS='$LIBSCALAPACK'") diff --git a/easybuild/easyblocks/p/picard.py b/easybuild/easyblocks/p/picard.py deleted file mode 100644 index 15481fd40e..0000000000 --- a/easybuild/easyblocks/p/picard.py +++ /dev/null @@ -1,90 +0,0 @@ -## -# Copyright 2009-2024 Ghent University -# -# This file is part of EasyBuild, -# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en), -# with support of Ghent University (http://ugent.be/hpc), -# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be), -# Flemish Research Foundation (FWO) (http://www.fwo.be/en) -# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en). -# -# https://github.com/easybuilders/easybuild -# -# EasyBuild is free software: you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation v2. -# -# EasyBuild is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. -# -# You should have received a copy of the GNU General Public License -# along with EasyBuild. If not, see . -## -""" -Support for building and installing picard, implemented as an easyblock. - -@author: Stijn De Weirdt (Ghent University) -@author: Dries Verdegem (Ghent University) -@author: Kenneth Hoste (Ghent University) -@author: Pieter De Baets (Ghent University) -@author: Jens Timmerman (Ghent University) -""" - -import os -import re -import shutil -from easybuild.tools import LooseVersion - -from easybuild.easyblocks.generic.tarball import Tarball -from easybuild.tools.build_log import EasyBuildError - - -class EB_picard(Tarball): - """Support for building and installing picard.""" - - def install_step(self): - """Install picard by copying required files""" - # recent version may contain more than just the picard-tools subdirectory - picard_tools_dir = 'picard-tools-%s' % self.version - if not re.search("%s/?$" % picard_tools_dir, self.cfg['start_dir']): - self.cfg['start_dir'] = os.path.join(self.cfg['start_dir'], picard_tools_dir) - if not os.path.exists(self.cfg['start_dir']): - raise EasyBuildError("Path %s to copy files from doesn't exist.", self.cfg['start_dir']) - - for jar in os.listdir(self.cfg['start_dir']): - src = os.path.join(self.cfg['start_dir'], jar) - dst = os.path.join(self.installdir, jar) - try: - shutil.copy2(src, dst) - self.log.info("Successfully copied %s to %s" % (src, dst)) - except OSError as err: - raise EasyBuildError("Failed to copy %s to %s (%s)", src, dst, err) - - def sanity_check_step(self): - """Custom sanity check for picard""" - # All versions prior to 1.124 have this jar file - if LooseVersion(self.version) < LooseVersion('1.124'): - jar_files = ['picard-%s' % self.version] - else: - # Starting with v1.124 a major structural change was made to picard - # All versions >= 1.124 now only have these jar files - jar_files = [ - 'htsjdk-%s' % self.version, - 'picard', - 'picard-lib' - ] - - custom_paths = { - 'files': ["%s.jar" % x for x in jar_files], - 'dirs': [], - } - - super(EB_picard, self).sanity_check_step(custom_paths=custom_paths) - - def make_module_extra(self): - """Add module entries specific to picard""" - txt = super(EB_picard, self).make_module_extra() - txt += self.module_generator.prepend_paths('PATH', '') - return txt diff --git a/easybuild/easyblocks/p/pyquante.py b/easybuild/easyblocks/p/pyquante.py deleted file mode 100644 index b48ccf2218..0000000000 --- a/easybuild/easyblocks/p/pyquante.py +++ /dev/null @@ -1,48 +0,0 @@ -## -# Copyright 2009-2024 Ghent University -# -# This file is part of EasyBuild, -# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en), -# with support of Ghent University (http://ugent.be/hpc), -# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be), -# Flemish Research Foundation (FWO) (http://www.fwo.be/en) -# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en). -# -# https://github.com/easybuilders/easybuild -# -# EasyBuild is free software: you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation v2. -# -# EasyBuild is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. -# -# You should have received a copy of the GNU General Public License -# along with EasyBuild. If not, see . -## -""" -EasyBuild support for PyQuante, implemented as an easyblock - -@author: Ward Poelmans (Ghent University) -""" - -from easybuild.easyblocks.generic.pythonpackage import PythonPackage -from easybuild.tools.modules import get_software_root - - -class EB_PyQuante(PythonPackage): - """Support for installing the PyQuante Python package.""" - - def configure_step(self): - """Check for Libint and use it if present""" - - root_libint = get_software_root("Libint") - if root_libint: - self.log.info("Building Libint extension") - self.cfg.update('installopts', "--enable-libint") - else: - self.log.warning("Not building Libint extension") - - super(EB_PyQuante, self).configure_step()