{bio}[foss/2025a] ImmuneBuilder v1.2

easybuild/easyconfigs/e/expecttest/expecttest-0.3.0-GCCcore-14.2.0.eb

@@ -0,0 +1,25 @@
+easyblock = 'PythonPackage'
+
+name = 'expecttest'
+version = '0.3.0'
+
+homepage = 'https://github.com/ezyang/expecttest'
+description = """This library implements expect tests (also known as "golden" tests). Expect tests are a method of
+ writing tests where instead of hard-coding the expected output of a test, you run the test to get the output, and
+ the test framework automatically populates the expected output. If the output of the test changes, you can rerun
+ the test with the environment variable EXPECTTEST_ACCEPT=1 to automatically update the expected output."""
+
+toolchain = {'name': 'GCCcore', 'version': '14.2.0'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['6e8512fb86523ada1f94fd1b14e280f924e379064bb8a29ee399950e513eeccd']
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('poetry', '2.1.2'),
+]
+dependencies = [
+    ('Python', '3.13.1'),
+]
+
+moduleclass = 'tools'

easybuild/easyconfigs/i/ImmuneBuilder/ANARCI-79f6c57-muscle5-compat.patch

@@ -0,0 +1,60 @@
+--- a/build_pipeline/FormatAlignments.py
++++ b/build_pipeline/FormatAlignments.py
+@@ -181,1 +181,1 @@
+-        pr = Popen( [ "muscle", "-in", ffile, "-gapopen", "-10", "-out", al_filename, ], stdout=PIPE, stderr=PIPE )
++        pr = Popen( [ "muscle", "-align", ffile, "-output", al_filename ], stdout=PIPE, stderr=PIPE )
+@@ -191,1 +191,11 @@
+-    start = ref_aligned.index( reference[0] )
++    # MUSCLE v5 may insert gap characters within a motif; search in degapped
++    # sequence and map the result back to the gapped alignment column index.
++    ref_degapped = ref_aligned.replace('-', '').replace('.', '')
++    motif_pos = ref_degapped.index(reference[0])
++    count, start = 0, 0
++    for i, c in enumerate(ref_aligned):
++        if count == motif_pos:
++            start = i
++            break
++        if c not in '-.':
++            count += 1
+--- a/setup.py
++++ b/setup.py
+@@ -10,3 +10,3 @@
+         # Post-installation routine
+-       ANARCI_LOC = os.path.join(site.getsitepackages()[0], 'anarci') # site-packages/ folder
++       ANARCI_LOC = os.path.join(self.install_lib, 'anarci')  # install target, not system site-packages
+         ANARCI_BIN = sys.executable.split('python')[0] # bin/ folder
+@@ -28,4 +28,21 @@
+         # Copy HMMs where ANARCI can find them
+-       shutil.copy( "curated_alignments/germlines.py", ANARCI_LOC )
+-       os.mkdir(os.path.join(ANARCI_LOC, "dat"))
+-       shutil.copytree( "HMMs", os.path.join(ANARCI_LOC, "dat/HMMs/") )
++       source_pkg_dir = os.path.join("..", "lib", "python", "anarci")
++       for package_dir in [source_pkg_dir, ANARCI_LOC]:
++           if os.path.isfile(package_dir):
++               os.remove(package_dir)
++           if not os.path.isdir(package_dir):
++               os.makedirs(package_dir)
++           shutil.copy("curated_alignments/germlines.py", os.path.join(package_dir, "germlines.py"))
++
++           dat_dir = os.path.join(package_dir, "dat")
++           hmms_dir = os.path.join(dat_dir, "HMMs")
++
++           if os.path.exists(dat_dir) and not os.path.isdir(dat_dir):
++               os.remove(dat_dir)
++           os.makedirs(dat_dir, exist_ok=True)
++
++           if os.path.isdir(hmms_dir):
++               shutil.rmtree(hmms_dir)
++           elif os.path.exists(hmms_dir):
++               os.remove(hmms_dir)
++           shutil.copytree("HMMs", hmms_dir)
+@@ -39,2 +57,4 @@
+         except OSError:
+             pass
++       finally:
++           os.chdir("..")
+@@ -50,1 +50,2 @@
+-     include_package_data = True,
++     include_package_data = True,
++     package_data={'anarci': ['germlines.py', 'dat/HMMs/**', 'dat/HMMs/**/**']},
+

easybuild/easyconfigs/i/ImmuneBuilder/ImmuneBuilder-1.2-foss-2025a-CUDA-12.8.0.eb

@@ -0,0 +1,97 @@
+easyblock = 'PythonBundle'
+
+name = 'ImmuneBuilder'
+version = '1.2'
+
+homepage = 'https://github.com/brennanaba/ImmuneBuilder'
+description = """Deep-learning models for predicting immune receptor protein structures
+(ABodyBuilder2, NanoBodyBuilder2, TCRBuilder2)."""
+
+toolchain = {'name': 'foss', 'version': '2025a'}
+versionsuffix = '-CUDA-12.8.0'
+
+# Public EasyBuild 2025a work is on PyTorch 2.9.1; there is no upstream/public
+# easyconfig or PR for PyTorch 2.6.0 on foss/2025a.
+# If your site only provides a module for PyTorch/OpenMM, switch those entries
+# to EXTERNAL_MODULE dependencies using the exact module names from `module avail`.
+
+dependencies = [
+    ('CUDA', '12.8.0', '', SYSTEM),
+    ('Python', '3.13.1'),
+    ('Python-bundle-PyPI', '2025.04'),
+    ('SciPy-bundle', '2025.06'),
+    ('Biopython', '1.85'),  # Required by anarci for Bio.SearchIO.HmmerIO
+    ('einops', '0.8.1'),
+    ('gemmi', '0.7.4'),
+    ('PyTorch', '2.9.1', '-CUDA-12.8.0'),
+    ('OpenMM', '8.4.0'),
+]
+
+builddependencies = [
+    # ANARCI setup.py runs build_pipeline/RUN_pipeline.sh and requires these tools in PATH.
+    ('HMMER', '3.4'),
+    ('MUSCLE', '5.3'),
+]
+
+exts_list = [
+    # cgi was removed in Python 3.13; pdbfixer requires the compatibility package.
+    ('legacy-cgi', '2.6.4', {
+        'modulename': 'cgi',
+        'source_tmpl': 'legacy_cgi-%(version)s-py3-none-any.whl',
+        'checksums': ['7e235ce58bf1e25d1fc9b2d299015e4e2cd37305eccafec1e6bac3fc04b878cd'],
+    }),
+    ('PDBFixer', '1.12', {
+        'source_urls': ['https://github.com/openmm/pdbfixer/archive/refs/tags/'],
+        'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}],
+        'modulename': 'pdbfixer',
+        'checksums': ['a5c0b05dfaf2cdcad3b8ffc9ee1e6a955628aade0dda653da04d4a12ba4fe3ec'],
+    }),
+    # ANARCI uses a custom install command (CustomInstallCommand) that:
+    # - runs build_pipeline/RUN_pipeline.sh (downloads IMGT germlines, builds HMMs with HMMER/MUSCLE)
+    # - copies generated HMMs into the package directory
+    # The patch (ANARCI-79f6c57-muscle5-compat.patch) fixes:
+    # (1) MUSCLE v5 CLI flags (setup.py originally used v3 args)
+    # (2) ANARCI_LOC uses self.install_lib instead of site.getsitepackages()[0]
+    # (3) adds finally: os.chdir("..") after the pipeline to restore CWD
+    # (4) adds package_data so pip includes germlines.py and HMMs in the wheel
+    # preinstallopts pre-runs the pipeline and stages files in the source tree
+    # so that pip's bdist_wheel picks them up before CustomInstallCommand runs.
+    ('anarci', '79f6c57', {
+        'source_urls': ['https://github.com/oxpig/ANARCI/archive/'],
+        'sources': ['79f6c575056dedef86cb8f405ebb039197923eec.zip'],
+        'patches': ['ANARCI-79f6c57-muscle5-compat.patch'],
+        'preinstallopts': (
+            'cd build_pipeline && bash RUN_pipeline.sh && '
+            'cp curated_alignments/germlines.py ../lib/python/anarci/ && '
+            'mkdir -p ../lib/python/anarci/dat && cp -r HMMs ../lib/python/anarci/dat/ && '
+            'cd .. && '
+        ),
+        'modulename': 'anarci',
+        'checksums': ['805f227cd165dd1930871ef98de48c30eaa24b4597be501a26d69e4d09a2d54e'],
+    }),
+    (name, version, {
+        'source_urls': ['https://github.com/brennanaba/ImmuneBuilder/archive/refs/tags/'],
+        'sources': ['%(version)s.tar.gz'],
+        'checksums': ['1f5d4952d8a558366ff27e0c05c19e858b2a19a0f802708345c8ecbdc7e252c6'],
+        'modulename': 'ImmuneBuilder',
+    }),
+]
+
+sanity_check_paths = {
+    'files': [
+        'bin/ABodyBuilder2',
+        'bin/NanoBodyBuilder2',
+        'bin/TCRBuilder2',
+    ],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/ImmuneBuilder'],
+}
+
+# Sanity checks: verify binaries and import, which confirms anarci is available
+sanity_check_commands = [
+    'ABodyBuilder2 --help',
+    'NanoBodyBuilder2 --help',
+    'TCRBuilder2 --help',
+]
+
+moduleclass = 'bio'
+

easybuild/easyconfigs/i/ImmuneBuilder/ImmuneBuilder-1.2-foss-2025a.eb

@@ -0,0 +1,111 @@
+easyblock = 'PythonBundle'
+
+name = 'ImmuneBuilder'
+version = '1.2'
+
+homepage = 'https://github.com/brennanaba/ImmuneBuilder'
+description = """Deep-learning models for predicting immune receptor protein structures
+(ABodyBuilder2, NanoBodyBuilder2, TCRBuilder2)."""
+
+toolchain = {'name': 'foss', 'version': '2025a'}
+
+# Public EasyBuild 2025a work is on PyTorch 2.9.1; there is no upstream/public
+# easyconfig or PR for PyTorch 2.6.0 on foss/2025a.
+# If your site only provides a module for PyTorch/OpenMM, switch those entries
+# to EXTERNAL_MODULE dependencies using the exact module names from `module avail`.
+
+dependencies = [
+    ('Python', '3.13.1'),
+    ('Python-bundle-PyPI', '2025.04'),
+    ('SciPy-bundle', '2025.06'),
+    ('Biopython', '1.85'),  # Required by anarci for Bio.SearchIO.HmmerIO
+    ('einops', '0.8.1'),
+    ('gemmi', '0.7.4'),
+    ('PyTorch', '2.9.1', '-CUDA-12.8.0'),
+    ('OpenMM', '8.4.0'),
+]
+
+builddependencies = [
+    # uv-build 0.7.22 requires rustc >= 1.86.
+    ('Rust', '1.91.1'),
+    ('maturin', '1.8.3'),
+    # ANARCI setup.py runs build_pipeline/RUN_pipeline.sh and requires these tools in PATH.
+    ('HMMER', '3.4'),
+    # Exception: no MUSCLE easyconfig exists for foss-2025a; use local GCCcore-14.2.0 recipe.
+    ('MUSCLE', '5.1.0', '', ('GCCcore', '14.2.0')),
+]
+
+use_pip = True
+
+exts_list = [
+    ('uv-build', '0.7.22', {
+        'source_urls': [PYPI_SOURCE],
+        'sources': ['uv_build-0.7.22.tar.gz'],
+        'modulename': 'uv_build',
+        'checksums': ['e7575036f987080a25a473971c0e6795c79e0b7bd04b95e5a35d5d51e19f3a6c'],
+    }),
+    # cgi was removed in Python 3.13; pdbfixer requires the compatibility package.
+    ('legacy-cgi', '2.6.4', {
+        'modulename': 'cgi',
+        'source_tmpl': 'legacy_cgi-%(version)s-py3-none-any.whl',
+        'checksums': ['7e235ce58bf1e25d1fc9b2d299015e4e2cd37305eccafec1e6bac3fc04b878cd'],
+    }),
+    ('PDBFixer', '1.12', {
+        'source_urls': ['https://github.com/openmm/pdbfixer/archive/refs/tags/'],
+        'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}],
+        'modulename': 'pdbfixer',
+        'checksums': ['a5c0b05dfaf2cdcad3b8ffc9ee1e6a955628aade0dda653da04d4a12ba4fe3ec'],
+    }),
+    # ANARCI uses a custom install command (CustomInstallCommand) that:
+    # - runs build_pipeline/RUN_pipeline.sh (downloads IMGT germlines, builds HMMs with HMMER/MUSCLE)
+    # - copies generated HMMs into the package directory
+    # The patch (ANARCI-79f6c57-muscle5-compat.patch) fixes:
+    # (1) MUSCLE v5 CLI flags (setup.py originally used v3 args)
+    # (2) ANARCI_LOC uses self.install_lib instead of site.getsitepackages()[0]
+    # (3) adds finally: os.chdir("..") after the pipeline to restore CWD
+    # (4) adds package_data so pip includes germlines.py and HMMs in the wheel
+    # preinstallopts pre-runs the pipeline and stages files in the source tree
+    # so that pip's bdist_wheel picks them up before CustomInstallCommand runs.
+    ('anarci', '79f6c57', {
+        'source_urls': ['https://github.com/oxpig/ANARCI/archive/'],
+        'sources': ['79f6c575056dedef86cb8f405ebb039197923eec.zip'],
+        'patches': ['ANARCI-79f6c57-muscle5-compat.patch'],
+        'preinstallopts': (
+            'cd build_pipeline && bash RUN_pipeline.sh && '
+            'cp curated_alignments/germlines.py ../lib/python/anarci/ && '
+            'mkdir -p ../lib/python/anarci/dat && cp -r HMMs ../lib/python/anarci/dat/ && '
+            'cd .. && '
+        ),
+        'modulename': 'anarci',
+        'checksums': ['805f227cd165dd1930871ef98de48c30eaa24b4597be501a26d69e4d09a2d54e'],
+    }),
+    (name, version, {
+        'source_urls': ['https://github.com/brennanaba/ImmuneBuilder/archive/refs/tags/'],
+        'sources': ['%(version)s.tar.gz'],
+        'checksums': ['1f5d4952d8a558366ff27e0c05c19e858b2a19a0f802708345c8ecbdc7e252c6'],
+        'modulename': 'ImmuneBuilder',
+    }),
+]
+
+sanity_check_paths = {
+    'files': [
+        'bin/ABodyBuilder2',
+        'bin/NanoBodyBuilder2',
+        'bin/TCRBuilder2',
+    ],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/ImmuneBuilder'],
+}
+
+# Sanity checks: verify binaries and import, which confirms anarci is available
+sanity_check_commands = [
+    'ABodyBuilder2 --help',
+    'NanoBodyBuilder2 --help',
+    'TCRBuilder2 --help',
+]
+
+moduleclass = 'bio'
+
+# uv-build installs a Rust binary that bypasses EB's RPATH linker wrapper.
+# It is only needed as a build backend, not at runtime. Remove to avoid RPATH sanity check failure.
+postinstallcmds = ['rm -f %(installdir)s/bin/uv-build']
+

easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.1.0-GCCcore-14.2.0.eb

@@ -0,0 +1,44 @@
+easyblock = 'MakeCp'
+
+name = 'MUSCLE'
+version = '5.1.0'
+
+homepage = 'https://drive5.com/muscle/'
+description = """MUSCLE is one of the best-performing multiple alignment programs
+ according to published benchmark tests, with accuracy and speed that are consistently
+ better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users
+ learn everything they need to know about MUSCLE in a few minutes-only a handful of
+ command-line options are needed to perform common alignment tasks."""
+
+toolchain = {'name': 'GCCcore', 'version': '14.2.0'}
+
+github_account = 'rcedgar'
+source_urls = [GITHUB_LOWER_SOURCE]
+sources = ['%(version)s.tar.gz']
+patches = ['MUSCLE-5.1.0-add_Aarch64_support.patch']
+checksums = [
+    {'5.1.0.tar.gz': '2bba8b06e3ccabf6465fa26f459763b2029d7e7b9596881063e3aaba60d9e87d'},
+    {'MUSCLE-5.1.0-add_Aarch64_support.patch': 'aa4c95d8c9dc7205d1d7257f38fce841d49379f87aa88d17df2a1e6ae7ebc9ef'},
+]
+
+builddependencies = [
+    ('binutils', '2.42'),
+]
+
+start_dir = 'src'
+
+# Use build environment defined by EasyBuild
+prebuildopts = "sed -i 's/$(CPPOPTS)/$(CPPOPTS) $(CXXFLAGS) $(CPPFLAGS)/g' Makefile &&"
+buildopts = "CPP=${CXX} CC=${CC}"
+
+files_to_copy = [(['Linux/muscle'], 'bin')]
+
+sanity_check_paths = {
+    'files': ['bin/muscle'],
+    'dirs': [],
+}
+
+sanity_check_commands = ["muscle -h"]
+
+moduleclass = 'bio'
+

easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.3-GCCcore-14.2.0.eb

@@ -0,0 +1,52 @@
+easyblock = 'MakeCp'
+
+name = 'MUSCLE'
+version = '5.3'
+
+homepage = 'https://drive5.com/muscle/'
+description = """MUSCLE is one of the best-performing multiple alignment programs
+ according to published benchmark tests, with accuracy and speed that are consistently
+ better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users
+ learn everything they need to know about MUSCLE in a few minutes-only a handful of
+ command-line options are needed to perform common alignment tasks."""
+
+toolchain = {'name': 'GCCcore', 'version': '14.2.0'}
+
+github_account = 'rcedgar'
+source_urls = [GITHUB_LOWER_SOURCE]
+# GitHub release tag is v5.3, while version is kept as 5.3 for module naming consistency.
+sources = [
+    {'download_filename': 'v%(version)s.tar.gz', 'filename': '%(version)s.tar.gz'},
+    {
+        'filename': 'vcxproj_make.py',
+        'download_filename': 'vcxproj_make.py',
+        'source_urls': ['https://raw.githubusercontent.com/rcedgar/vcxproj_make/806d016'],
+        'extract_cmd': 'cp %s %(builddir)s/muscle-%(version)s/src/',
+    },
+]
+checksums = [
+    {'5.3.tar.gz': '74b22a94e630b16015c2bd9ae83aa2be2c2048d3e41f560b2d4a954725c81968'},
+    {'vcxproj_make.py': '902735703004c47705ffa389329378f237fecb154945b489edf6abe260c6694f'},
+]
+
+builddependencies = [
+    ('binutils', '2.42'),
+]
+
+# MUSCLE 5.3 uses vcxproj_make.py to generate Makefile/build rules.
+# Vendor the script as a source to avoid runtime network access.
+start_dir = '.'
+build_cmd = 'cd src && python3 vcxproj_make.py --openmp && sed -i "s/ -static//g" Makefile && make'
+
+
+files_to_copy = [(['bin/muscle'], 'bin')]
+
+sanity_check_paths = {
+    'files': ['bin/muscle'],
+    'dirs': [],
+}
+
+sanity_check_commands = ["muscle -h"]
+
+moduleclass = 'bio'
+