{bio,lib}[foss/2022a] AlphaPulldown v0.30.7, cctbx-base v2023.5

easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.7-foss-2022a.eb

@@ -0,0 +1,69 @@
+# created by Denis Kristak (Inuits)
+easyblock = 'PythonBundle'
+
+name = 'AlphaPulldown'
+version = '0.30.7'
+
+homepage = 'https://github.com/KosinskiLab/AlphaPulldown'
+description = """AlphaPulldown is a Python package that streamlines protein-protein
+interaction screens and high-throughput modelling of higher-order oligomers using AlphaFold-Multimer"""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('OpenMM', '8.0.0'),
+    ('Kalign', '3.3.5'),
+    ('PyYAML', '6.0'),
+    ('cctbx-base', '2023.5'),
+    ('jax', '0.3.25'),  # also provides absl-py
+    ('Biopython', '1.79'),
+    ('h5py', '3.7.0'),
+    ('IPython', '8.5.0'),
+    ('JupyterLab', '3.5.0'),
+    ('matplotlib', '3.5.2'),
+    ('TensorFlow', '2.11.0'),
+    ('tqdm', '4.64.0'),
+    ('dm-tree', '0.1.8'),
+    ('py3Dmol', '2.0.1.post1'),
+    ('AlphaFold', '2.3.4', '-ColabFold'),  # must match with AlphaFold dep of ColabFold
+    ('ColabFold', '1.5.2'),
+]
+
+use_pip = True
+
+# note: rely on extensions included in AlphaFold installation (PDBFixer, dm-haiku, contextlib2, ml-collections)
+exts_list = [
+    ('importlib-resources', '5.13.0', {
+        'source_tmpl': 'importlib_resources-%(version)s.tar.gz',
+        'checksums': ['82d5c6cca930697dbbd86c93333bb2c2e72861d4789a11c2662b933e5ad2b528'],
+        'modulename': 'importlib_resources',
+    }),
+    (name, version, {
+        'sources': ['%(namelower)s-%(version)s.tar.gz'],
+        'patches': ['AlphaPulldown-%(version)s_AlphaFold-ColabFold-deps.patch'],
+        'checksums': [
+            {'alphapulldown-0.30.7.tar.gz': 'e089e4b3b238fe2874c7e4cc38368a6784f3e4664ad11b0b3d9088d1cdfa7c96'},
+            {'AlphaPulldown-0.30.7_AlphaFold-ColabFold-deps.patch':
+             'f9d756c7e6a34016697361ac5d94a04afa26b666199cb7326c7e58dc1ea649af'},
+        ],
+        # loosen up strict version requirements for required Python packages,
+        # and remove copies of AlphaFold + ColabFold that are included (to use provided dependencies instead)
+        'preinstallopts': "sed -i 's/==/>=/g' setup.cfg && rm -rf alphafold colabold alphapulldown/ColabFold && ",
+    }),
+]
+
+fix_python_shebang_for = ['bin/*.py']
+
+postinstallcmds = ["cp -a %(builddir)s/AlphaPulldown-*/example_data %(installdir)s/"]
+
+sanity_pip_check = True
+
+sanity_check_paths = {
+    'files': ['bin/run_multimer_jobs.py', 'bin/rename_colab_search_a3m.py'],
+    'dirs': ['example_data', 'lib/python%(pyshortver)s/site-packages/alphapulldown'],
+}
+
+sanity_check_commands = ["run_multimer_jobs.py --help 2>&1 | grep 'USAGE:'"]
+
+moduleclass = 'bio'

easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.7_AlphaFold-ColabFold-deps.patch

@@ -0,0 +1,82 @@
+use $EBROOTALPHAFOLD set by AlphaFold dependency provided by EasyBuild to determine path to run_alphafold.py script,
+patch setup.cfg to not install alphafold/colafold packages + not install stereo_chemical_props.txt as data file (since it's provided by AlphaFold dependency)
+author: Kenneth Hoste (HPC-UGent)
+diff -ru alphapulldown-0.30.7.orig/alphapulldown/create_individual_features.py alphapulldown-0.30.7/alphapulldown/create_individual_features.py
+--- alphapulldown-0.30.7.orig/alphapulldown/create_individual_features.py	2023-04-19 13:33:53
++++ alphapulldown-0.30.7/alphapulldown/create_individual_features.py	2023-08-08 20:59:37
+@@ -42,19 +42,7 @@
+     return module
+
+
+-PATH_TO_RUN_ALPHAFOLD = os.path.join(
+-    os.path.dirname(alphafold.__file__), "run_alphafold.py"
+-)
+-
+-try:
+-    run_af = load_module(PATH_TO_RUN_ALPHAFOLD, "run_alphafold")
+-except FileNotFoundError:
+-    PATH_TO_RUN_ALPHAFOLD = os.path.join(
+-        os.path.dirname(os.path.dirname(alphafold.__file__)), "run_alphafold.py"
+-    )
+-
+-    run_af = load_module(PATH_TO_RUN_ALPHAFOLD, "run_alphafold")
+-
++run_af = get_run_alphafold()
+
+ flags = run_af.flags
+ flags.DEFINE_bool("save_msa_files", False, "save msa output or not")
+diff -ru alphapulldown-0.30.7.orig/alphapulldown/utils.py alphapulldown-0.30.7/alphapulldown/utils.py
+--- alphapulldown-0.30.7.orig/alphapulldown/utils.py	2023-05-24 16:31:29
++++ alphapulldown-0.30.7/alphapulldown/utils.py	2023-08-08 20:59:52
+@@ -310,9 +310,13 @@
+     return module
+
+ def get_run_alphafold():
+-    PATH_TO_RUN_ALPHAFOLD = os.path.join(
+-        os.path.dirname(alphafold.__file__), "run_alphafold.py"
+-    )
++    ebrootalphafold = os.getenv('EBROOTALPHAFOLD')
++    if ebrootalphafold:
++        PATH_TO_RUN_ALPHAFOLD = os.path.join(ebrootalphafold, 'bin', 'run_alphafold.py')
++    else:
++        PATH_TO_RUN_ALPHAFOLD = os.path.join(
++            os.path.dirname(alphafold.__file__), "run_alphafold.py"
++        )
+
+     try:
+         run_af = load_module(PATH_TO_RUN_ALPHAFOLD, "run_alphafold")
+@@ -323,4 +327,4 @@
+
+         run_af = load_module(PATH_TO_RUN_ALPHAFOLD, "run_alphafold")
+
+-    return run_af
+\ No newline at end of file
++    return run_af
+diff -ru alphapulldown-0.30.7.orig/setup.cfg alphapulldown-0.30.7/setup.cfg
+--- alphapulldown-0.30.7.orig/setup.cfg	2023-06-21 14:14:42
++++ alphapulldown-0.30.7/setup.cfg	2023-08-08 21:01:04
+@@ -13,14 +13,10 @@
+ [options]
+ packages = 
+ 	alphapulldown
+-	alphafold
+-	colabfold
+ 	analysis_pipeline
+ 	af2plots
+ package_dir = 
+ 	alphapulldown = ./alphapulldown
+-	alphafold = ./alphafold/alphafold
+-	colabfold = ./alphapulldown/ColabFold/colabfold
+ 	analysis_pipeline = ./alphapulldown/analysis_pipeline
+ 	af2plots = ./alphapulldown/analysis_pipeline/af2_plots/af2plots
+ include_package_data = True
+@@ -49,9 +45,6 @@
+ [options.packages.find]
+ where = ./
+ exclude = test*
+-
+-[options.data_files]
+-lib/python3.8/site-packages/alphafold/common/ = stereo_chemical_props.txt
+
+ [egg_info]
+ tag_build = 

easybuild/easyconfigs/c/cctbx-base/cctbx-base-2023.5-foss-2022a.eb

@@ -0,0 +1,92 @@
+easyblock = 'Binary'
+
+name = 'cctbx-base'
+version = '2023.5'
+
+homepage = 'https://github.com/cctbx/cctbx_project'
+description = "Computational Crystallography Toolbox"
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+source_urls = ['https://github.com/cctbx/cctbx_project/releases/download/v2023.5/']
+sources = ['cctbx-%(version)s.tar.gz']
+patches = ['cctbx-base-%(version)s_do-not-use-non-public-boost-python-function.patch']
+checksums = [
+    {'cctbx-2023.5.tar.gz': '9983a4296e27f5c344555f079170a9abfc1513a3788a8e6087ae156003c8b2af'},
+    {'cctbx-base-2023.5_do-not-use-non-public-boost-python-function.patch':
+     '6e1a6669e5ddf94ed8d68c863c03013bc8c9239f8946381722e4de2a9a0442ec'},
+]
+
+builddependencies = [
+    ('SCons', '4.4.0'),
+    ('Eigen', '3.4.0'),
+    ('pybind11', '2.9.2'),
+]
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('Boost', '1.79.0'),
+    ('Boost.Python-NumPy', '1.79.0'),
+    ('HDF5', '1.12.2'),
+    ('LibTIFF', '4.3.0'),
+]
+
+extract_sources = True
+
+local_adaptbx_sconscript = 'modules/cctbx_project/boost_adaptbx/SConscript'
+
+local_bootstrap_build_cmd = "python bootstrap.py build --builder=cctbx --with-python $EBROOTPYTHON/bin/python "
+local_bootstrap_build_cmd += "--no-boost-src --nproc %(parallel)s "
+local_bootstrap_build_cmd += "--config-flags='--use_environment_flags' --config-flags='--skip_phenix_dispatchers' "
+
+local_libtbx_python_cmd = "./build/bin/libtbx.python lib/libtbx/auto_build/conda_build/install_build.py "
+local_libtbx_python_cmd += "--prefix %(installdir)s --sp-dir %(installdir)s/lib/python%(pyshortver)s/site-packages "
+local_libtbx_python_cmd += "--ext-dir %(installdir)s/lib/python%(pyshortver)s/lib-dynload --preserve-egg-dir "
+
+install_cmds = [
+    # prepare
+    "rm -r modules/{boost,eigen,scons}",
+    "mkdir -p modules/boost && cd modules/boost && ln -s $EBROOTBOOST/include/boost",
+    "ln -s lib/libtbx/auto_build/bootstrap.py",
+    "export CCTBX_SKIP_CHEMDATA_CACHE_REBUILD=1",
+
+    # patch SConscript scripts to use Boost* dependencies
+    "sed -i 's/build_boost_libs = True/build_boost_libs = False/g' %s" % local_adaptbx_sconscript,
+    """sed -i "s/'boost_python'/'boost_python%%(pymajver)s%%(pyminver)s'/g" %s""" % local_adaptbx_sconscript,
+    """sed -i "s/'boost_numpy'/'boost_numpy%%(pymajver)s%%(pyminver)s'/g" %s""" % local_adaptbx_sconscript,
+    """sed -i 's/"boost_python"/"boost_python%(pymajver)s%(pyminver)s"/g' modules/dxtbx/SConscript""",
+
+    # build
+    local_bootstrap_build_cmd,
+    "cd build && ./bin/libtbx.configure cma_es crys3d fable rstbx spotinder",
+    "cd build && ./bin/libtbx.scons -j %(parallel)s",
+
+    # patch bootstrap.py to not blindly overwrite $LD_LIBRARY_PATH
+    # cfr. https://github.com/cctbx/cctbx_project/commit/c53e5ec15b3a7172087dce11c1a908f03144b45c
+    r"sed 's@\(export LD_LIBRARY_PATH=\.\./base/lib\)\n@\1:$LD_LIBRARY_PATH\n@g' bootstrap.py",
+
+    # install
+    "mkdir -p %(installdir)s/{bin,include,lib,share}",
+    "mkdir -p %(installdir)s/lib/python%(pyshortver)s/{lib-dynload,site-packages}",
+    local_libtbx_python_cmd,
+
+    # install Python bindings
+    "cd modules/cctbx_project && pip install --no-deps --ignore-installed --prefix %(installdir)s .",
+]
+
+sanity_check_paths = {
+    'files': ['bin/cctbx.find_distances', 'bin/cctbx.getting_started', 'bin/cctbx.lattice_symmetry',
+              'include/boost_adaptbx/type_id_eq.h', 'lib/libcctbx.%s' % SHLIB_EXT,
+              'lib/libscitbx_minpack.%s' % SHLIB_EXT, 'lib/libspotfinder.%s' % SHLIB_EXT],
+    'dirs': ['include/cctbx', 'include/scitbx', 'include/smtbx', 'lib/python%(pyshortver)s/lib-dynload',
+             'lib/python%(pyshortver)s/site-packages', 'share/cctbx'],
+}
+
+sanity_check_commands = [
+    "cctbx.getting_started",
+    "cctbx.lattice_symmetry",
+] + ["python -c 'import %s'" % x for x in ['boost_adaptbx', 'crys3d', 'libtbx', 'scitbx', 'spotfinder']]
+
+modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'}
+
+moduleclass = 'lib'

easybuild/easyconfigs/c/cctbx-base/cctbx-base-2023.5_do-not-use-non-public-boost-python-function.patch

@@ -0,0 +1,18 @@
+strip out optional code that relies on non-public cxxabi_cxa_demangle_is_broken function in Boost.Python;
+fix for missing symbol _ZN5boost6python29cxxabi_cxa_demangle_is_brokenEv
+author: Simon Branford (University of Birmingham)
+--- cctbx-2023.5.orig/modules/cctbx_project/boost_adaptbx/meta_ext.cpp.orig   2023-06-27 09:10:15.541028000 +0100
++++ cctbx-2023.5/modules/cctbx_project/boost_adaptbx/meta_ext.cpp    2023-06-27 09:11:30.755613353 +0100
+@@ -298,12 +298,6 @@
+ #if defined(__llvm__)
+     result += "__llvm__\n";
+ #endif
+-#if defined(BOOST_PYTHON_HAVE_CXXABI_CXA_DEMANGLE_IS_BROKEN) \
+-    && !defined(USE_CONDA) \
+-    && !defined(__MINGW32__) // workaround for MinGW linking problem
+-    result += "boost::python::cxxabi_cxa_demangle_is_broken(): "
+-            + to_str(boost::python::cxxabi_cxa_demangle_is_broken()) + nl;
+-#endif
+ #if defined(__GXX_WEAK__)
+     result += "__GXX_WEAK__ = " + to_str(__GXX_WEAK__) + nl;
+ #endif