sync with develop (20241226)

easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-13.3.0-Java-21.0.2.eb → easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-13.3.0-Java-17.eb

@@ -22,7 +22,7 @@ checksums = [
 
 builddependencies = [('binutils', '2.42')]
 
-dependencies = [('Java', '21.0.2', '', SYSTEM)]
+dependencies = [('Java', '17', '', SYSTEM)]
 
 configopts = '--disable-examples --disable-csharp --disable-python'
 

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

@@ -0,0 +1,57 @@
+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'),
+]
+
+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_check_paths = {
+    'files': ['bin/bonito'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = [
+    "bonito --help",
+    "bonito download --help",
+]
+
+moduleclass = 'bio'

easybuild/easyconfigs/d/DjVuLibre/DjVuLibre-3.5.28-GCCcore-12.3.0.eb

@@ -25,6 +25,7 @@ builddependencies = [
 dependencies = [
     ('libjpeg-turbo', '2.1.5.1'),
     ('LibTIFF', '4.5.0'),
+    ('librsvg', '2.58.0'),
 ]
 
 _bins = ['bin/%s' % x for x in ['any2djvu', 'bzz', 'c44', 'cjb2', 'cpaldjvu', 'csepdjvu', 'ddjvu', 'djvm', 'djvmcvt',

easybuild/easyconfigs/e/EasyBuild/EasyBuild-0.5.0.0beta1.eb

@@ -0,0 +1,59 @@
+easyblock = 'EB_EasyBuildMeta'
+
+name = 'EasyBuild'
+version = '0.5.0.0beta1'
+
+homepage = 'https://easybuild.io'
+description = """EasyBuild is a software build and installation framework
+ written in Python that allows you to install software in a structured,
+ repeatable and robust way."""
+
+toolchain = SYSTEM
+
+sources = [
+    {
+        'filename': 'easybuild-framework-v%s.tar.gz' % version[2:],
+        'git_config': {
+            'url': 'https://github.com/easybuilders',
+            'repo_name': 'easybuild-framework',
+            'tag': 'easybuild-framework-v%s' % version[2:],
+            'keep_git_dir': True,
+        },
+    },
+    {
+        'filename': 'easybuild-easyblocks-v%s.tar.gz' % version[2:],
+        'git_config': {
+            'url': 'https://github.com/easybuilders',
+            'repo_name': 'easybuild-easyblocks',
+            'tag': 'easybuild-easyblocks-v%s' % version[2:],
+            'keep_git_dir': True,
+        },
+    },
+    {
+        'filename': 'easybuild-easyconfigs-v%s.tar.gz' % version[2:],
+        'git_config': {
+            'url': 'https://github.com/easybuilders',
+            'repo_name': 'easybuild-easyconfigs',
+            'tag': 'easybuild-easyconfigs-v%s' % version[2:],
+            'keep_git_dir': True,
+        },
+    },
+]
+checksums = [
+    None,
+    None,
+    None,
+]
+
+# EasyBuild is a (set of) Python packages, so it depends on Python
+# usually, we want to use the system Python, so no actual Python dependency is listed
+allow_system_deps = [('Python', SYS_PYTHON_VERSION)]
+
+local_pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2])
+
+sanity_check_paths = {
+    'files': ['bin/eb'],
+    'dirs': ['lib/python%s/site-packages' % local_pyshortver],
+}
+
+moduleclass = 'tools'

easybuild/easyconfigs/f/Fiji/Fiji-2.14.0-Java-11.eb

@@ -0,0 +1,52 @@
+easyblock = 'PackedBinary'
+
+name = 'Fiji'
+version = '2.14.0'
+versionsuffix = '-Java-%(javaver)s'
+
+homepage = 'https://fiji.sc/'
+description = """Fiji is an image processing package—a 'batteries-included' distribution of
+ ImageJ, bundling a lot of plugins which facilitate scientific image analysis.
+This release is based on ImageJ-2.1.0 and Fiji-2.1.1"""
+
+toolchain = SYSTEM
+
+source_urls = ['https://downloads.imagej.net/fiji/releases/%(version)s']
+sources = ['%(namelower)s-%(version)s-nojre.zip']
+checksums = ['1dcf6efd7a2c99b70ab921bea3b9e7c74ef99acf35b9857199de7f9c424187db']
+
+dependencies = [('Java', '11', '', SYSTEM)]
+
+postinstallcmds = [
+    # Remove binaries for other platforms
+    'rm %(installdir)s/{ImageJ-win32.exe,ImageJ-win64.exe}',
+    # Enable any update site (edit existing site with same parameters to enable it)
+    # Full list at https://imagej.github.io/list-of-update-sites/
+    '%(installdir)s/ImageJ-linux64 --default-gc --java-home "$EBROOTJAVA/lib/server/" --headless'
+    ' --update edit-update-site "ImageScience" https://sites.imagej.net/ImageScience/',
+    '%(installdir)s/ImageJ-linux64 --default-gc --java-home "$EBROOTJAVA/lib/server/" --headless'
+    ' --update edit-update-site "3D ImageJ Suite" https://sites.imagej.net/Tboudier/',
+    '%(installdir)s/ImageJ-linux64 --default-gc --java-home "$EBROOTJAVA/lib/server/" --headless'
+    ' --update edit-update-site "ilastik" https://sites.imagej.net/Ilastik/',
+    # Add a new update site
+    # '%(installdir)s/ImageJ-linux64 --headless --update add-update-site "New Name"'
+    # ' https://site.url/NewName/',
+    # Update the installation
+    '%(installdir)s/ImageJ-linux64 --default-gc --java-home "$EBROOTJAVA/lib/server/" --headless --update update',
+]
+
+sanity_check_paths = {
+    'files': ['ImageJ-linux64'],
+    'dirs': [],
+}
+
+modloadmsg = """
+Additional plugins can be installed in your $HOME/.plugins folder or requested to user support
+Use ImageJ/Fiji in headless mode in your scripts with the command `ImageJ-linux64 --headless`
+More information at https://imagej.net/Headless
+Also for Fiji 2.14.0 the arguments `--default-gc --java-home "$EBROOTJAVA/lib/server/"`
+should always be used when running `ImageJ-linux64` commands to avoid errors like:
+`Could not load Java library` and `Unrecognized option: -Xincgc`.
+"""
+
+moduleclass = 'vis'

easybuild/easyconfigs/h/Hydra/Hydra-1.3.2-foss-2023a-with-plugins.eb

@@ -0,0 +1,97 @@
+easyblock = 'PythonBundle'
+
+name = 'Hydra'
+version = '1.3.2'
+versionsuffix = '-with-plugins'
+
+homepage = "https://hydra.cc/"
+description = """
+Hydra is an open-source Python framework that simplifies the development of
+research and other complex applications. The key feature is the ability to
+dynamically create a hierarchical configuration by composition and override it
+through config files and the command line. The name Hydra comes from its
+ability to run multiple similar jobs - much like a Hydra with multiple heads.
+"""
+
+github_account = 'facebookresearch'
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('Java', '17', '', SYSTEM),  # needed by ANTLR runtime
+    ('hatchling', '1.18.0'),
+]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('PyYAML', '6.0'),  # needed by omegaconf
+    ('tqdm', '4.66.1'),
+    ('SciPy-bundle', '2023.07'),
+    ('Greenlet', '3.0.2'),
+    ('SQLAlchemy', '2.0.25'),
+    ('Mako', '1.2.4'),
+]
+
+exts_list = [
+    ('alembic', '1.12.1', {
+        'checksums': ['bca5877e9678b454706347bc10b97cb7d67f300320fa5c3a94423e8266e2823f'],
+    }),
+    ('autopage', '0.5.2', {
+        'checksums': ['826996d74c5aa9f4b6916195547312ac6384bac3810b8517063f293248257b72'],
+    }),
+    ('cliff', '4.3.0', {
+        'checksums': ['fc5b6ebc8fb815332770b2485ee36c09753937c37cce4f3227cdd4e10b33eacc'],
+    }),
+    ('cmd2', '2.4.3', {
+        'checksums': ['71873c11f72bd19e2b1db578214716f0d4f7c8fa250093c601265a9a717dee52'],
+    }),
+    ('cmaes', '0.10.0', {
+        'checksums': ['48afc70df027114739872b50489ae6b32461c307b92d084a63c7090a9742faf9'],
+    }),
+    ('colorlog', '6.7.0', {
+        'checksums': ['bd94bd21c1e13fac7bd3153f4bc3a7dc0eb0974b8bc2fdf1a989e474f6e582e5'],
+    }),
+    ('pyperclip', '1.8.2', {
+        'checksums': ['105254a8b04934f0bc84e9c24eb360a591aaf6535c9def5f29d92af107a9bf57'],
+    }),
+    ('prettytable', '3.9.0', {
+        'checksums': ['f4ed94803c23073a90620b201965e5dc0bccf1760b7a7eaf3158cab8aaffdf34'],
+    }),
+    ('stevedore', '5.1.0', {
+        'checksums': ['a54534acf9b89bc7ed264807013b505bf07f74dbe4bcfa37d32bd063870b087c'],
+    }),
+    ('optuna', '2.10.1', {
+        'checksums': ['8a12009b57757c1070b3bff2261c24824d6430c22926dd1e2ace33b3deff555f'],
+    }),
+    ('antlr4-python3-runtime', '4.9', {
+        'modulename': 'antlr4',
+        'checksums': ['02d9afb720c13c52b336234286966cdf5aff704f230a513e635adb0d94de97ae'],
+    }),
+    ('omegaconf', '2.3.0', {
+        'checksums': ['d5d4b6d29955cc50ad50c46dc269bcd92c6e00f5f90d23ab5fee7bfca4ba4cc7'],
+    }),
+    ('read_version', '0.3.2', {
+        'checksums': ['3f2d30852bce9174b244f7f29aaebf4e79904c6ed51a19716325015ff306ce3f'],
+    }),
+    ('hydra-optuna-sweeper', '1.2.0', {
+        'modulename': False,
+        'checksums': ['f20b56dfdc4db9f84f3b502c8e60a5269967197c4df4c28653cf17f71b2136ce'],
+    }),
+    ('cloudpickle', '3.0.0', {
+        'checksums': ['996d9a482c6fb4f33c1a35335cf8afd065d2a56e973270364840712d9131a882'],
+    }),
+    ('submitit', '1.5.0', {
+        'checksums': ['2766868e71656b1e278a42f33bced74faebf2c525dba74f4cc43be8cbef6c588'],
+    }),
+    ('hydra-submitit-launcher', '1.2.0', {
+        'modulename': False,
+        'checksums': ['e14c8eb46d020fac60ba25f82bcc368dc55851d2683dc95c88631ffcf15e4a34'],
+    }),
+    ('hydra-core', version, {
+        'modulename': 'hydra',
+        'checksums': ['8a878ed67216997c3e9d88a8e72e7b4767e81af37afb4ea3334b269a4390a824'],
+    }),
+]
+
+moduleclass = 'data'