{data}[intel/2020a] pySCENIC v0.10.3, dask v2.18.1, scikit-learn v0.23.1, bokeh v2.0.2 w/ Python 3.8.2

easybuild/easyconfigs/b/bokeh/bokeh-2.0.2-intel-2020a-Python-3.8.2.eb

@@ -0,0 +1,43 @@
+easyblock = 'PythonBundle'
+
+name = 'bokeh'
+version = '2.0.2'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'https://github.com/bokeh/bokeh'
+description = "Statistical and novel interactive HTML plots for Python"
+
+toolchain = {'name': 'intel', 'version': '2020a'}
+
+dependencies = [
+    ('Python', '3.8.2'),
+    ('PyYAML', '5.3'),
+    ('Pillow', '7.0.0', versionsuffix),
+    ('SciPy-bundle', '2020.03', versionsuffix),
+]
+
+use_pip = True
+
+exts_default_options = {'source_urls': [PYPI_SOURCE]}
+
+exts_list = [
+    ('tornado', '6.0.4', {
+        'checksums': ['0fe2d45ba43b00a41cd73f8be321a44936dc1aba233dee979f17a042b83eb6dc'],
+    }),
+    ('typing-extensions', '3.7.4.2', {
+        'source_tmpl': 'typing_extensions-%(version)s.tar.gz',
+        'checksums': ['79ee589a3caca649a9bfd2a8de4709837400dfa00b6cc81962a1e6a1815969ae'],
+    }),
+    (name, version, {
+        'checksums': ['d9248bdb0156797abf6d04b5eac581dcb121f5d1db7acbc13282b0609314893a'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/bokeh'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_pip_check = True
+
+moduleclass = 'tools'

easybuild/easyconfigs/d/dask/dask-2.18.1-intel-2020a-Python-3.8.2.eb

@@ -0,0 +1,82 @@
+easyblock = 'PythonBundle'
+
+name = 'dask'
+version = '2.18.1'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'https://dask.org/'
+description = """Dask natively scales Python. Dask provides advanced parallelism for analytics, enabling performance
+ at scale for the tools you love."""
+
+toolchain = {'name': 'intel', 'version': '2020a'}
+
+dependencies = [
+    ('Python', '3.8.2'),
+    ('PyYAML', '5.3'),
+    ('SciPy-bundle', '2020.03', versionsuffix),
+    ('bokeh', '2.0.2', versionsuffix),
+]
+
+use_pip = True
+
+exts_default_options = {'source_urls': [PYPI_SOURCE]}
+
+exts_list = [
+    ('fsspec', '0.7.4', {
+        'checksums': ['7075fde6d617cd3a97eac633d230d868121a188a46d16a0dcb484eea0cf2b955'],
+    }),
+    ('toolz', '0.10.0', {
+        'checksums': ['08fdd5ef7c96480ad11c12d472de21acd32359996f69a5259299b540feba4560'],
+    }),
+    ('locket', '0.2.0', {
+        'checksums': ['1fee63c1153db602b50154684f5725564e63a0f6d09366a1cb13dffcec179fb4'],
+    }),
+    ('partd', '1.1.0', {
+        'checksums': ['6e258bf0810701407ad1410d63d1a15cfd7b773fd9efe555dac6bb82cc8832b0'],
+    }),
+    ('HeapDict', '1.0.1', {
+        'checksums': ['8495f57b3e03d8e46d5f1b2cc62ca881aca392fd5cc048dc0aa2e1a6d23ecdb6'],
+    }),
+    ('zict', '2.0.0', {
+        'checksums': ['8e2969797627c8a663575c2fc6fcb53a05e37cdb83ee65f341fc6e0c3d0ced16'],
+    }),
+    ('tblib', '1.6.0', {
+        'checksums': ['229bee3754cb5d98b4837dd5c4405e80cfab57cb9f93220410ad367f8b352344'],
+    }),
+    ('msgpack', '1.0.0', {
+        'checksums': ['9534d5cc480d4aff720233411a1f765be90885750b07df772380b34c10ecb5c0'],
+    }),
+    ('cloudpickle', '1.4.1', {
+        'checksums': ['0b6258a20a143603d53b037a20983016d4e978f554ec4f36b3d0895b947099ae'],
+    }),
+    (name, version, {
+        'checksums': ['8ed21e2344419fad7c6f648123f6f56cf2480d0ac4fae92d9063adb321f1c490'],
+    }),
+    ('distributed', '2.18.0', {
+        'checksums': ['902f098fb7558f035333804a5aeba2fb26a2a715388808205a17cbb2e02e0558'],
+    }),
+    ('dask-mpi', '2.0.0', {
+        'checksums': ['774cd2d69e5f7154e1fa133c22498062edd31507ffa2ea19f4ab4d8975c27bc3'],
+    }),
+    ('immutables', '0.14', {
+        'checksums': ['a0a1cc238b678455145bae291d8426f732f5255537ed6a5b7645949704c70a78'],
+    }),
+    ('contextvars', '2.4', {
+        'checksums': ['f38c908aaa59c14335eeea12abea5f443646216c4e29380d7bf34d2018e2c39e'],
+    }),
+    ('docrep', '0.2.7', {
+        'checksums': ['c48939ae14d79172839a5bbaf5a570add47f6cc44d2c18f6b1fac8f1c38dec4d'],
+    }),
+    ('dask-jobqueue', '0.7.1', {
+        'checksums': ['d32ddf3e3c7db29ace102037fa5f61c8db2d945176454dc316a6ffdb8bbfe88b'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/dask-%s' % x for x in ['mpi', 'scheduler', 'ssh', 'worker']],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_pip_check = True
+
+moduleclass = 'data'

easybuild/easyconfigs/p/pySCENIC/pySCENIC-0.10.3-intel-2020a-Python-3.8.2.eb

@@ -0,0 +1,85 @@
+easyblock = 'PythonBundle'
+
+name = 'pySCENIC'
+version = '0.10.3'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'https://github.com/aertslab/pySCENIC'
+description = """pySCENIC is a lightning-fast python implementation of the SCENIC
+pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables
+biologists to infer transcription factors, gene regulatory networks and
+cell types from single-cell RNA-seq data."""
+
+toolchain = {'name': 'intel', 'version': '2020a'}
+
+dependencies = [
+    ('Python', '3.8.2'),
+    ('PyYAML', '5.3'),
+    ('numba', '0.50.0', versionsuffix),
+    ('Arrow', '0.17.1', versionsuffix),
+    ('scikit-learn', '0.23.1', versionsuffix),
+    ('tqdm', '4.47.0'),
+    ('networkx', '2.4', versionsuffix),
+    ('h5py', '2.10.0', versionsuffix),
+    ('dask', '2.18.1', versionsuffix),
+]
+
+use_pip = True
+
+exts_default_options = {'source_urls': [PYPI_SOURCE]}
+
+exts_list = [
+    ('cytoolz', '0.10.1', {
+        'checksums': ['82f5bba81d73a5a6b06f2a3553ff9003d865952fcb32e1df192378dd944d8a5c'],
+    }),
+    ('dill', '0.3.2', {
+        'source_tmpl': 'dill-%(version)s.zip',
+        'checksums': ['6e12da0d8e49c220e8d6e97ee8882002e624f1160289ce85ec2cc0a5246b3a2e'],
+    }),
+    ('multiprocessing_on_dill', '3.5.0a4', {
+        'checksums': ['d6d50c300ff4bd408bb71eb78725e60231039ee9b3d0d9bb7697b9d0e15045e7'],
+    }),
+    ('frozendict', '1.2', {
+        'checksums': ['774179f22db2ef8a106e9c38d4d1f8503864603db08de2e33be5b778230f6e45'],
+    }),
+    ('arboreto', '0.1.5', {
+        'checksums': ['a78c73b367eaae38dadeba150e52ac98aec6fc916df703ce61b79d27fe1015f9'],
+    }),
+    ('boltons', '20.2.0', {
+        'checksums': ['d367506c0b32042bb1ee3bf7899f2dcc8492dceb42ce3727b89e174d85bffe6e'],
+    }),
+    ('interlap', '0.2.6', {
+        'checksums': ['a8585a165bf7e94d4d262811b4cb00674059414c50afc7561c949b0feb78fa09'],
+    }),
+    ('umap-learn', '0.4.6', {
+        'modulename': 'umap',
+        'checksums': ['4276da9a039c79fa5b4f8d3515a8ccaaccf11a2f59ce8d15baf9d2015a5e82b3'],
+    }),
+    ('numpy_groupies', '0.9.10', {
+        'checksums': ['a6835c252b7bd489e0f701f8bf5bc880c647ef251e3b434998b95a8aecc9b68a'],
+    }),
+    ('loompy', '3.0.6', {
+        'checksums': ['58e9763b8ab1af2a4a0e3805d120458b5184fd2b0f3031657ecce33c63ca4c46'],
+    }),
+    ('pyscenic', version, {
+        'patches': ['pySCENIC-%(version)s_fix-pyarrow-FeatherReader.patch'],
+        'checksums': [
+            '517c4fadf6198ba0202116f1c419d61c4d4491fc4099b611fbe738845fe4acc9',  # pyscenic-0.10.3.tar.gz
+            # pySCENIC-0.10.3_fix-pyarrow-FeatherReader.patch
+            '022e69a384771a1389d176db699cc97f5a3c8ee43502a49f0335b82c1932e0e5',
+        ],
+        # strip out version restrictions for required Python packages
+        'preinstallopts': "sed -i 's/[=>]=[0-9].*//g' requirements.txt && ",
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/pyscenic'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ["pyscenic --help"]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'

easybuild/easyconfigs/p/pySCENIC/pySCENIC-0.10.3_fix-pyarrow-FeatherReader.patch

@@ -0,0 +1,17 @@
+fix compatibilty with PyArrow 0.17.1, where FeatherReader was moved from pyarrow.feather to pyarrow.lib
+author: Kenneth Hoste (HPC-UGent)
+--- pyscenic-0.10.3/src/pyscenic/rnkdb.py.orig	2020-08-11 14:55:53.212511866 +0200
++++ pyscenic-0.10.3/src/pyscenic/rnkdb.py	2020-08-11 14:56:02.932604710 +0200
+@@ -9,7 +9,11 @@
+ from operator import itemgetter
+ from .genesig import GeneSignature
+ from cytoolz import memoize
+-from pyarrow.feather import write_feather, FeatherReader
++from pyarrow.feather import write_feather
++try:
++    from pyarrow.feather import FeatherReader
++except ImportError:
++    from pyarrow.lib import FeatherReader
+ from tqdm import tqdm
+
+

easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.1-intel-2020a-Python-3.8.2.eb

@@ -0,0 +1,46 @@
+easyblock = 'PythonBundle'
+
+name = 'scikit-learn'
+version = '0.23.1'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'https://scikit-learn.org/stable/index.html'
+description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world,
+building upon numpy, scipy, and matplotlib. As a machine-learning module,
+it provides versatile tools for data mining and analysis in any field of science and engineering.
+It strives to be simple and efficient, accessible to everybody, and reusable in various contexts."""
+
+toolchain = {'name': 'intel', 'version': '2020a'}
+
+dependencies = [
+    ('Python', '3.8.2'),
+    ('SciPy-bundle', '2020.03', versionsuffix)
+]
+
+use_pip = True
+
+exts_default_options = {'source_urls': [PYPI_SOURCE]}
+
+exts_list = [
+    ('pytoml', '0.1.21', {
+        'checksums': ['8eecf7c8d0adcff3b375b09fe403407aa9b645c499e5ab8cac670ac4a35f61e7'],
+    }),
+    ('flit-core', '2.3.0', {
+        'source_tmpl': 'flit_core-%(version)s.tar.gz',
+        'checksums': ['a50bcd8bf5785e3a7d95434244f30ba693e794c5204ac1ee908fc07c4acdbf80'],
+    }),
+    ('flit', '2.3.0', {
+        'checksums': ['017012b809ec489918afd68af7a70bd7c8c770c87b60159d875c126866e97a4b'],
+    }),
+    ('threadpoolctl', '2.1.0', {
+        'checksums': ['ddc57c96a38beb63db45d6c159b5ab07b6bced12c45a1f07b2b92f272aebfa6b'],
+    }),
+    (name, version, {
+        'modulename': 'sklearn',
+        'checksums': ['e3fec1c8831f8f93ad85581ca29ca1bb88e2da377fb097cf8322aa89c21bc9b8'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'data'