Merge pull request #21979 from pavelToman/20241205182031_new_pr_Bonit…

…o081

{bio}[foss/2023a] Bonito v0.8.1, ont-remora v3.3.0 w/ CUDA 12.1.1

easybuild/easyconfigs/b/Bonito/Bonito-0.8.1-foss-2023a-CUDA-12.1.1.eb

@@ -0,0 +1,61 @@
+easyblock = 'PythonBundle'
+
+name = 'Bonito'
+version = '0.8.1'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://github.com/nanoporetech/bonito'
+description = "Convolution Basecaller for Oxford Nanopore Reads"
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('CUDA', '12.1.1', '', SYSTEM),
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('SciPy-bundle', '2023.07'),
+    ('PyTorch', '2.1.2', versionsuffix),
+    ('edlib', '1.3.9'),
+    ('ont-fast5-api', '4.1.2'),
+    ('ont-remora', '3.3.0', versionsuffix),
+    ('python-parasail', '1.3.4'),
+    ('pod5-file-format', '0.3.10'),
+    ('Pysam', '0.22.0'),
+    ('tqdm', '4.66.1'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('fast-ctc-decode', '0.3.6', {
+        'source_tmpl': 'fast_ctc_decode-0.3.6-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl',
+        'unpack_sources': False,
+        'checksums': ['f49994a475866edf0e61f0d9e1b41185c035ba559b8c2aa68f83342d2c80ee6b'],
+    }),
+    ('mappy', '2.28', {
+        'checksums': ['0ebf7a5d62bd668f5456028215e26176e180ca68161ac18d4f7b48045484cebb'],
+    }),
+    ('ont_koi', '0.4.4', {
+        'source_tmpl': 'ont_koi-0.4.4-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl',
+        'modulename': 'koi',
+        'checksums': ['e5d7c93b26363a3d4e3778f972d1f149447adbde91925e8876a97e7a63774e28'],
+    }),
+    ('ont-bonito', version, {
+        'modulename': 'bonito',
+        'checksums': ['26df86ee233bf020b549177e1e2aaa7ad7d99cf0927d79ab3fa31c1670d09ba6'],
+    }),
+]
+
+sanity_pip_check = True
+
+sanity_check_paths = {
+    'files': ['bin/bonito'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = [
+    "bonito --help",
+    "bonito download --help",
+]
+
+moduleclass = 'bio'

easybuild/easyconfigs/o/ont-remora/ont-remora-3.3.0-foss-2023a-CUDA-12.1.1.eb

@@ -0,0 +1,62 @@
+easyblock = 'PythonBundle'
+
+name = 'ont-remora'
+version = '3.3.0'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://github.com/nanoporetech/remora'
+description = """Methylation/modified base calling separated from basecalling. Remora primarily
+provides an API to call modified bases for basecaller programs such as Bonito.
+Remora also provides the tools to prepare datasets, train modified base models
+and run simple inference."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('CUDA', '12.1.1', '', SYSTEM),
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('ONNX-Runtime', '1.19.2', versionsuffix),
+    ('PyTorch', '2.1.2', versionsuffix),
+    ('scikit-learn', '1.3.1'),
+    ('tqdm', '4.66.1'),
+    ('python-parasail', '1.3.4'),
+    ('polars', '0.20.2'),
+    ('Pysam', '0.22.0'),
+    ('pod5-file-format', '0.3.10'),
+    ('statsmodels', '0.14.1'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('thop', '0.1.1.post2209072238', {
+        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+        'checksums': ['01473c225231927d2ad718351f78ebf7cffe6af3bed464c4f1ba1ef0f7cdda27'],
+    }),
+    ('mizani', '0.9.3', {
+        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+        'checksums': ['ac5d49b913de88dc2fb28d82141e9777b97407a6971a158f758093ad5bb820a1'],
+    }),
+    ('plotnine', '0.12.4', {
+        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+        'checksums': ['12748f346f107c33f3e0658ac46fbb052205ae7e97ffaf52be68310e5d29f799'],
+    }),
+    (name, version, {
+        'modulename': 'remora',
+        'checksums': ['3c899e7333ae33ebec31c8a59650ab4d553e8a62c0abf7b03899e2ee9a0bc88a'],
+    }),
+]
+
+sanity_pip_check = True
+
+sanity_check_paths = {
+    'files': ['bin/remora'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = [
+    ('remora', '--help'),
+]
+
+moduleclass = 'bio'