Work update for #16, #29 and #169

169_Bonito/Bonito-0.4.0-fosscuda-2020b.eb

@@ -0,0 +1,129 @@
+# author: Denis Kristak (INUITS)
+easyblock = 'PythonBundle'
+
+name = 'Bonito'
+version = '0.7.1'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://github.com/nanoporetech/bonito'
+description = "Convolution Basecaller for Oxford Nanopore Reads"
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('CUDA', '11.7.0', '', SYSTEM),
+    ('SciPy-bundle', '2022.05'),
+    ('PyTorch', '1.12.1', '-CUDA-%(cudaver)s'),
+    ('h5py', '3.7.0'),
+    ('Mako', '1.2.0'),
+    ('PyYAML', '6.0'),
+    ('python-parasail', '1.3.3'),
+    ('tqdm', '4.64.0'),
+    ('apex', '20230702', '-CUDA-%(cudaver)s'),
+    ('minimap2', '2.24'),
+    ('CuPy', '12.1.0', '-CUDA-%(cudaver)s'),
+    ('GenomeWorks', '2021.02.2'),
+    ('pyspoa', '0.0.9'),
+    ('ont-fast5-api', '3.3.0'),
+    ('ont-remora', '2.1.2'),
+    ('Pysam', '0.20.0'),
+    ('pod5-file-format', '0.1.8'),
+]
+
+use_pip = True
+
+# strip out too strict version requirements for dependencies
+local_bonito_preinstallopts = "sed -i 's/[><=]=.*//g' requirements.txt && "
+# fix requirements for stuff we include as a proper dependency
+local_bonito_preinstallopts += "sed -i 's/genomeworks-cuda-10-2/genomeworks/g' requirements.txt && "
+local_bonito_preinstallopts += "sed -i 's/cupy-cuda102/cupy/g' requirements.txt && "
+local_bonito_preinstallopts += "sed -i 's/numpy~=[0-9.]*/numpy/g' requirements.txt && "
+local_bonito_preinstallopts += "sed -i 's/torch~=[0-9.]*/torch/g' requirements.txt && "
+local_bonito_preinstallopts += "export PATH=%(installdir)s/bin/:$PATH && "
+
+exts_list = [
+    ('python-editor', '1.0.4', {
+        'modulename': 'editor',
+        'checksums': ['51fda6bcc5ddbbb7063b2af7509e43bd84bfc32a4ff71349ec7847713882327b'],
+    }),
+    ('alembic', '1.6.4', {
+        'checksums': ['becb572c6701c90ca249f97fc1ae231468cc9516df367a350901eeb9310a8d43'],
+    }),
+    ('cmd2', '1.5.0', {
+        'checksums': ['701a8c9975c4abc45e5d13906ab149f959f812869106347323a3f89ac0e82a62'],
+    }),
+    ('prettytable', '2.1.0', {
+        'checksums': ['5882ed9092b391bb8f6e91f59bcdbd748924ff556bb7c634089d5519be87baa0'],
+    }),
+    ('cliff', '3.7.0', {
+        'preinstallopts': "sed -i'' 's/cmd2.*/cmd2/g' requirements.txt && ",
+        'checksums': ['389c81960de13f05daf1cbd546f33199e86c518ba4266c79ec7a153a280980ea'],
+    }),
+    ('colorlog', '5.0.1', {
+        'checksums': ['f17c013a06962b02f4449ee07cfdbe6b287df29efc2c9a1515b4a376f4e588ea'],
+    }),
+    ('greenlet', '1.1.0', {
+        'checksums': ['c87df8ae3f01ffb4483c796fe1b15232ce2b219f0b18126948616224d3f658ee'],
+    }),
+    ('SQLAlchemy', '1.4.15', {
+        'checksums': ['0ff100c75cd175f35f4d24375a0b3d82461f5b1af5fc8d112ef0e5ceea8049e6'],
+    }),
+    ('cmaes', '0.8.2', {
+        'checksums': ['1c04ba23ded925ef13b96f42cfbd667a905ea5b80754c750e6448b9fcda96a5d'],
+    }),
+    ('optuna', '2.7.0', {
+        'checksums': ['eb1595108ec444e840deb0037351074144fecb7a4eff6870fc11569ab782cfc6'],
+    }),
+    ('colorama', '0.4.4', {
+        'checksums': ['5941b2b48a20143d2267e95b1c2a7603ce057ee39fd88e7329b0c292aa16869b'],
+    }),
+    ('pyperclip', '1.8.2', {
+        'checksums': ['105254a8b04934f0bc84e9c24eb360a591aaf6535c9def5f29d92af107a9bf57'],
+    }),
+    ('importlib_metadata', '4.0.1', {
+        'checksums': ['8c501196e49fb9df5df43833bdb1e4328f64847763ec8a50703148b73784d581'],
+    }),
+    ('stevedore', '3.3.0', {
+        'checksums': ['3a5bbd0652bf552748871eaa73a4a8dc2899786bc497a2aa1fcb4dcdb0debeee'],
+    }),
+    ('fast-ctc-decode', '0.3.5', {
+        'source_tmpl': 'fast_ctc_decode-%(version)s-cp38-cp38-manylinux2010_x86_64.whl',
+        'unpack_sources': False,
+    }),
+    ('mappy', '2.24', {
+    }),
+    ('seqdist', '0.0.3', {
+        'preinstallopts': "sed -i 's/cupy-cuda102//g' settings.ini && sed -i 's/[<>=]=[0-9].*//g' settings.ini && ",
+        'checksums': ['bdbbea6ebba1c6dd6698d46e23ba7858f93a7cdf0c7cbc2ea66660291acb044f'],
+    }),
+    ('crf-beam', '0.0.1a0', {
+        'modulename': 'kbeam',
+        'sources': ['crf_beam-%(version)s-cp38-cp38-manylinux1_x86_64.whl'],
+        'unpack_sources': False,
+        'checksums': ['0cba80ff4d7f90595f498921cf904736e3bce558dba80de5611874d89e72312e'],
+    }),
+    ('networkx', '2.5.1', {
+        'checksums': ['109cd585cac41297f71103c3c42ac6ef7379f29788eb54cb751be5a663bb235a'],
+    }),
+    ('ont-bonito', version, {
+        'modulename': 'bonito',
+        'preinstallopts': local_bonito_preinstallopts,
+        'checksums': ['429310d56e2d7dabd91a9a9c972504a0aa2b6d6469563b14d4aae30adfe9a87e'],
+    }),
+]
+
+sanity_pip_check = True
+
+sanity_check_paths = {
+    'files': ['bin/bonito'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = [
+    "bonito --help",
+    "bonito convert --help",
+    "bonito download --help",
+]
+
+moduleclass = 'bio'

169_Bonito/CuPy/CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb

@@ -0,0 +1,68 @@
+easyblock = 'PythonBundle'
+
+name = 'CuPy'
+version = '12.1.0'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://cupy.dev'
+description = "CuPy is an open-source array library accelerated with NVIDIA CUDA."
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+builddependencies = [
+    ('pytest', '7.3.2'),
+]
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+    ('CUDA', '11.7.0', '', SYSTEM),
+    ('cuDNN', '8.4.1.50', versionsuffix, SYSTEM),
+    ('NCCL', '2.12.12', versionsuffix),
+    ('cuTENSOR', '1.6.1.5', versionsuffix, SYSTEM),
+    # Adding cuSPARSELt currently makes the build fail. Keeping it around for later versions to pick up.
+    # ('cuSPARSELt', '0.3.0.3', versionsuffix, SYSTEM),
+]
+
+use_pip = True
+
+exts_default_options = {'source_urls': [PYPI_LOWER_SOURCE]}
+
+# A bunch of the tests are failing or are just having problems.
+_skip_tests = [
+    'tests/cupyx_tests/scipy_tests',
+    'tests/cupyx_tests/distributed_tests',
+    'tests/cupyx_tests/tools_tests',
+    'tests/example_tests',
+    'tests/cupy_tests/testing_tests/test_parameterized.py',
+    'tests/cupy_tests/fft_tests/test_fft.py',
+]
+_ignore_list = ' --ignore='.join(_skip_tests)
+
+_deselect_tests = [
+    'tests/cupy_tests/core_tests/test_carray.py::TestCArray32BitBoundary_param_',
+    # float16 has too low precision for these tests as they are written
+    # See https://github.com/easybuilders/easybuild-easyconfigs/pull/17526#issuecomment-1470843170 for details.
+    'tests/cupy_tests/linalg_tests/test_product.py::TestProduct',
+]
+_deselect_list = ' --deselect='.join(_deselect_tests)
+
+exts_list = [
+    ('fastrlock', '0.8.1', {
+    }),
+    ('cupy', version, {
+        # Must run tests here since the required version of pytest is a builddep
+        # Note! test_cudnn and some others will likely fail on T4 GPUs due to out of memory.
+        'runtest': 'export CUPY_TEST_GPU_LIMIT=1 CUPY_CACHE_DIR="%%(builddir)s" && '
+                   'pytest --ignore=%s --deselect=%s tests' % (_ignore_list, _deselect_list),
+        'testinstall': True,
+    }),
+]
+
+sanity_check_commands = [
+    "python -c 'import cupy'",
+]
+
+sanity_pip_check = True
+
+moduleclass = 'lib'

169_Bonito/CuPy/pytest-7.2.2-GCCcore-11.2.0.eb

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+easyblock = 'PythonBundle'
+
+name = 'pytest'
+version = '7.3.2'
+
+homepage = 'https://docs.pytest.org/en/latest/'
+description = """The pytest framework makes it easy to write small,
+readable tests, and can scale to support complex functional testing for
+applications and libraries."""
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+
+builddependencies = [
+    ('binutils', '2.38'),
+]
+
+dependencies = [
+    ('Python', '3.10.4'),
+]
+
+use_pip = True
+
+exts_default_options = {'source_urls': [PYPI_LOWER_SOURCE]}
+
+# Note! Some of the file system related tests may fail on shared file systems.
+# Notably TestPOSIXLocalPath.test_copy_stat_file, TestPOSIXLocalPath.test_copy_stat_dir
+# and test_source_mtime_long_long are known to fail on GPFS
+# Build with buildpath and tmpdir set to a local file system to avoid this
+# or use --ignore-test-failures
+_skip_tests = [
+    'testing/io/test_terminalwriter.py',
+    'testing/test_terminal.py',
+    'testing/test_debugging.py',
+    'testing/test_config.py',
+    'testing/test_helpconfig.py',
+]
+_ignore_tests = ' --ignore='.join(_skip_tests)
+
+exts_list = [
+    ('setuptools-scm', '7.1.0', {
+        'source_tmpl': 'setuptools_scm-%(version)s.tar.gz',
+        'checksums': ['6c508345a771aad7d56ebff0e70628bf2b0ec7573762be9960214730de278f27'],
+    }),
+    ('flit-core', '3.9.0', {
+        'source_tmpl': 'flit_core-%(version)s.tar.gz',
+    }),
+    ('flit-scm', '1.7.0', {
+        'source_tmpl': 'flit_scm-%(version)s.tar.gz',
+        'checksums': ['961bd6fb24f31bba75333c234145fff88e6de0a90fc0f7e5e7c79deca69f6bb2'],
+    }),
+    ('exceptiongroup', '1.1.2', {
+    }),
+    ('hypothesis', '6.80.0', {
+    }),
+    ('elementpath', '4.1.4', {
+    }),
+    ('xmlschema', '2.3.1', {
+    }),
+    (name, version, {
+    }),
+]
+
+sanity_check_commands = [
+    "python -c 'import pytest'",
+    'cd %%(builddir)s/%%(name)s/%%(name)s-%%(version)s && %%(installdir)s/bin/pytest --ignore=%s testing'
+    % _ignore_tests,
+]
+
+sanity_pip_check = True
+
+moduleclass = 'lib'

169_Bonito/GenomeWorks-2021.02.2-fosscuda-2020b.eb

@@ -0,0 +1,99 @@
+# author: Denis Kristak (INUITS)
+easyblock = 'CMakePythonPackage'
+
+name = 'GenomeWorks'
+version = '2021.02.2'
+local_commit = '691380d'  # corresponds to 2021.02.2 tag
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://github.com/clara-parabricks/GenomeWorks'
+description = "SDK for GPU accelerated genome assembly and analysis"
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+toolchainopts = {'pic': True}
+
+sources = [{
+    'filename': SOURCE_TAR_GZ,
+    'git_config': {
+        'url': 'https://github.com/clara-parabricks',
+        'repo_name': name,
+        'commit': local_commit,
+        'recursive': True,
+    },
+}]
+# no checksum for source tarball because it's created locally via 'git clone'
+checksums = [None]
+
+builddependencies = [
+    ('CMake', '3.24.3'),
+    ('Doxygen', '1.9.4'),
+]
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('CUDA', '11.7.0', '', SYSTEM),
+    ('Autoconf', '2.71'),
+    ('matplotlib', '3.5.2'),
+    ('SciPy-bundle', '2022.05'),
+    ('networkx', '2.8.4'),
+    ('tqdm', '4.64.0'),
+]
+
+# add missing include to a file
+preconfigopts = "sed -i'' 's/#include <exception>/#include <exception>\\n#include <stdexcept>/g'"
+preconfigopts += " %(builddir)s/GenomeWorks/3rdparty/spoa/src/alignment_engine.cpp && """
+
+preconfigopts += "sed -i 's/==/>=/g' %(builddir)s/GenomeWorks/pygenomeworks/requirements.txt && "
+preconfigopts += "sed -i 's/~=/>=/g' %(builddir)s/GenomeWorks/pygenomeworks/requirements.txt && "
+
+# instruction from GenomeWorks' readme
+configopts = "-Dgw_cuda_gen_all_arch=OFF "
+configopts += " -Dgw_build_shared=ON "
+
+# no test targets
+skipsteps = ['test']
+
+exts_defaultclass = 'PythonPackage'
+
+exts_default_options = {
+    'download_dep_fail': True,
+    'use_pip': True,
+    'sanity_pip_check': True,
+}
+
+local_genomeworks_preinstallopts = "sed -i 's/[=~]=/>=/g' requirements.txt && "
+local_genomeworks_preinstallopts += "export GW_INSTALL_DIR=%(installdir)s && "
+local_genomeworks_preinstallopts += "export GW_VERSION=%(version)s && "
+local_genomeworks_preinstallopts += "export GW_ROOT_DIR=%(builddir)s/GenomeWorks && "
+
+exts_list = [
+    ('sortedcollections', '2.1.0', {
+        'source_urls': [PYPI_SOURCE],
+        'checksums': ['d8e9609d6c580a16a1224a3dc8965789e03ebc4c3e5ffd05ada54a2fed5dcacd'],
+    }),
+    ('genomeworks', version, {
+        'sources': ['GenomeWorks-%(version)s.tar.gz'],
+        # no checksum for source tarball because it's created locally via 'git clone'
+        'checksums': [None],
+        'start_dir': 'pygenomeworks',
+        'preinstallopts': local_genomeworks_preinstallopts,
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/cudamapper', 'bin/cudapoa', 'bin/genome_simulator',
+              'lib/libgwbase.%s' % SHLIB_EXT, 'lib/libgwio.%s' % SHLIB_EXT],
+    'dirs': ['benchmarks', 'docs', 'include/claraparabricks/genomeworks',
+             'lib/python%(pyshortver)s/site-packages', 'samples', 'tests'],
+}
+
+sanity_check_commands = [
+    "cudamapper --help",
+    "cudapoa --help",
+    "genome_simulator --help",
+    "python -c 'import genomeworks'",
+]
+
+modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'}
+
+moduleclass = 'bio'