Merge pull request #12448 from deniskristak/20210322172017_new_pr_cel…

…l2locationv005alpha

{tools}[fosscuda/2020b] cell2location v0.05-alpha, dill v0.3.3, Seaborn 0.10.0, ... w/ Python 3.8.6

easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb

@@ -0,0 +1,133 @@
+# Author: Denis Krišťák (INUITS)
+
+easyblock = 'PythonBundle'
+
+name = 'cell2location'
+version = '0.05-alpha'
+local_nodejsver = '-nodejs-12.19.0'
+
+homepage = 'https://github.com/BayraktarLab/cell2location/'
+description = """Comprehensive mapping of tissue cell architecture via integrated 
+single cell and spatial transcriptomics (cell2location model)"""
+
+toolchain = {'name': 'fosscuda', 'version': '2020b'}
+
+builddependencies = [
+    ('Bison', '3.7.1'),
+]
+
+dependencies = [
+    ('Python', '3.8.6'),
+    ('Java', '11', '', True),
+    ('SciPy-bundle', '2020.11'),
+    ('leidenalg', '0.8.3'),
+    ('hyperopt', '0.2.5'),
+    ('CMake', '3.18.4'),
+    ('dill', '0.3.3'),
+    ('IPython', '7.18.1'),
+    ('Seaborn', '0.11.1'),
+    ('matplotlib', '3.3.3'),
+    ('libgpuarray', '0.7.6'),
+    ('PyMC3', '3.11.1'),
+    ('request', '2.88.1', local_nodejsver),
+    ('PyTables', '3.6.1'),
+    ('PyTorch', '1.7.1'),
+    ('statsmodels', '0.12.1'),
+    ('numba', '0.52.0'),
+    ('Theano', '1.1.2', '-PyMC'),
+    ('umap-learn', '0.4.6'),
+    ('pyro-api', '0.1.2'),
+    ('pyro-ppl', '1.5.2'),
+]
+
+preinstallopts = "sed -i 's/theano/Theano-PyMC/g' setup.py && "
+
+use_pip = True
+
+exts_default_options = {
+    'download_dep_fail': True,
+    'sanity_pip_check': True,
+    'use_pip': True,
+}
+
+exts_list = [
+    ('opt-einsum', '3.3.0', {
+        'source_tmpl': 'opt_einsum-%(version)s.tar.gz',
+        'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'],
+    }),
+    ('pytoml', '0.1.21', {
+        'checksums': ['8eecf7c8d0adcff3b375b09fe403407aa9b645c499e5ab8cac670ac4a35f61e7'],
+    }),
+    ('get_version', '2.1', {
+        'use_pip': False,
+        'checksums': ['8156b526c2557537b8ca82241fa2b82b3da25939627398f6567dee31ba9725bc'],
+    }),
+    ('legacy-api-wrap', '1.2', {
+        'use_pip': False,
+        'checksums': ['034a44612da7e9943d3964363a98937ab54d55e3301075374abe0d521eb8101b'],
+    }),
+    ('descartes', '1.1.0', {
+        'checksums': ['135a502146af5ed6ff359975e2ebc5fa4b71b5432c355c2cafdc6dea1337035b'],
+    }),
+    ('mizani', '0.7.1', {
+        'checksums': ['97eea665d17fdc6c827b832925c094839e1ef7bf65b3aa47105e772b6eca9b0a'],
+    }),
+    ('anndata', '0.7.5', {
+        'checksums': ['2113a7463388013023f153e1a1446add4182883e3320b6e37dda18ee6210e038'],
+    }),
+    ('ipykernel', '5.3.4', {
+        'checksums': ['9b2652af1607986a1b231c62302d070bc0534f564c393a5d9d130db9abbbe89d'],
+    }),
+    ('nose', '1.3.7', {
+        'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'],
+    }),
+    ('natsort', '7.1.0', {
+        'checksums': ['33f3f1003e2af4b4df20908fe62aa029999d136b966463746942efbfc821add3'],
+    }),
+    ('palettable', '3.3.0', {
+        'checksums': ['72feca71cf7d79830cd6d9181b02edf227b867d503bec953cf9fa91bf44896bd'],
+    }),
+    ('scanpy', '1.6.0', {
+        'checksums': ['542d1f1fc0471e7312d4349142e1c2eee4a465cd514fe4e3337be166f425fa55'],
+    }),
+    ('louvain', '0.7.0', {
+        'checksums': ['9734fc6bf8c15546d685a8c6d7d7ca0574cad4cb641e9ca91c3334028658f7c6'],
+    }),
+    ('loompy', '3.0.6', {
+        'checksums': ['58e9763b8ab1af2a4a0e3805d120458b5184fd2b0f3031657ecce33c63ca4c46'],
+    }),
+    ('bbknn', '1.3.12', {
+        'checksums': ['7dc5257baa278fc92349ac7865674ce70802dc4e3afdafed87a099dff9e91159'],
+    }),
+    ('stdlib-list', '0.8.0', {
+        'checksums': ['a1e503719720d71e2ed70ed809b385c60cd3fb555ba7ec046b96360d30b16d9f'],
+    }),
+    ('sinfo', '0.3.1', {
+        'checksums': ['e1b2358808aded7b2ff00ea0cd4e6a2d978fb2a44ee9b15ac23d64a81bf62706'],
+    }),
+    ('plotnine', '0.7.0', {
+        'checksums': ['8ee67cbf010ccea32670760e930b7b02177030a89ccdf85e35d156a96ce36cd3'],
+    }),
+    ('numpy-groupies', '0.9.13', {
+        'modulename': 'numpy_groupies',
+        'source_tmpl': 'numpy_groupies-%(version)s.tar.gz',
+        'checksums': ['7b17b291322353f07c51598512d077e3731da0a048cfa8f738f3460d1ef0658d'],
+    }),
+    ('annoy', '1.17.0', {
+        'checksums': ['9891e264041d1dcf3af42f67fbb16cb273c5404bc8c869d0915a3087f71d58dd'],
+    }),
+    (name, version, {
+        'source_urls': ['https://github.com/BayraktarLab/cell2location/archive/'],
+        'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
+        'checksums': ['2df1fe2b2b4ec5fcebc6c1d6146ce0cd79115bd14059b0ae882a41f1029a4efc'],
+    }),
+]
+
+sanity_pip_check = True
+
+sanity_check_paths = {
+    'files': ['bin/loompy', 'bin/scanpy'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+moduleclass = 'bio'

easybuild/easyconfigs/d/dill/dill-0.3.3-GCCcore-10.2.0.eb

@@ -0,0 +1,29 @@
+# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham.
+easyblock = 'PythonPackage'
+
+# Author: Denis Krišťák (INUITS)
+
+name = 'dill'
+version = '0.3.3'
+
+homepage = 'https://pypi.org/project/dill/'
+description = """dill extends python's pickle module for serializing and de-serializing python objects to the majority
+ of the built-in python types. Serialization is the process of converting an object to a byte stream, and the inverse
+ of which is converting a byte stream back to on python object hierarchy."""
+
+toolchain = {'name': 'GCCcore', 'version': '10.2.0'}
+
+sources = [SOURCE_ZIP]
+checksums = ['efb7f6cb65dba7087c1e111bb5390291ba3616741f96840bfc75792a1a9b5ded']
+
+builddependencies = [('binutils', '2.35')]
+
+dependencies = [
+    ('Python', '3.8.6'),
+]
+
+use_pip = True
+download_dep_fail = True
+sanity_pip_check = True
+
+moduleclass = 'data'

easybuild/easyconfigs/r/request/request-2.88.1-fosscuda-2020b-nodejs-12.19.0.eb

@@ -0,0 +1,31 @@
+# Author: Denis Krišťák (INUITS)
+
+easyblock = 'Binary'
+
+name = 'request'
+version = '2.88.1'
+local_nodejsver = '12.19.0'
+versionsuffix = '-nodejs-%s' % local_nodejsver
+
+homepage = 'https://github.com/request/request/'
+description = """Request is designed to be the simplest way possible to make http calls. 
+    It supports HTTPS and follows redirects by default."""
+
+toolchain = {'name': 'fosscuda', 'version': '2020b'}
+
+source_urls = ['https://github.com/request/request/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['6506ec33a673f6a5542a950be65b02b23c8e8cda21847c19ee67dee4fdc7adc4']
+
+dependencies = [
+    ('nodejs', local_nodejsver),
+]
+
+install_cmd = 'npm install --prefix %(installdir)s -g v%(version)s.tar.gz'
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/node_modules/%(namelower)s'],
+}
+
+moduleclass = 'tools'

easybuild/easyconfigs/s/statsmodels/statsmodels-0.12.1-fosscuda-2020b.eb

@@ -0,0 +1,32 @@
+# Author: Denis Krišťák (INUITS)
+
+easyblock = 'PythonBundle'
+
+name = 'statsmodels'
+version = '0.12.1'
+
+homepage = 'https://www.statsmodels.org/'
+description = """Statsmodels is a Python module that allows users to explore data, estimate statistical models,
+and perform statistical tests."""
+
+toolchain = {'name': 'fosscuda', 'version': '2020b'}
+
+dependencies = [
+    ('Python', '3.8.6'),
+    ('SciPy-bundle', '2020.11'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('patsy', '0.5.1', {
+        'checksums': ['f115cec4201e1465cd58b9866b0b0e7b941caafec129869057405bfe5b5e3991'],
+    }),
+    (name, version, {
+        'checksums': ['a271b4ccec190148dccda25f0cbdcbf871f408fc1394a10a7dc1af4a62b91c8e'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'math'

easybuild/easyconfigs/u/umap-learn/umap-learn-0.4.6-fosscuda-2020b.eb

@@ -0,0 +1,32 @@
+# Author: Denis Krišťák (INUITS)
+
+easyblock = 'PythonPackage'
+
+name = 'umap-learn'
+version = '0.4.6'
+
+homepage = 'https://pypi.org/project/umap-learn/'
+description = """Uniform Manifold Approximation and Projection (UMAP) is a 
+dimension reduction technique that can be used for visualisation similarly to t-SNE, 
+but also for general non-linear dimension reduction."""
+
+toolchain = {'name': 'fosscuda', 'version': '2020b'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['4276da9a039c79fa5b4f8d3515a8ccaaccf11a2f59ce8d15baf9d2015a5e82b3']
+
+dependencies = [
+    ('Python', '3.8.6'),
+    ('SciPy-bundle', '2020.11'),
+    ('scikit-learn', '0.23.2'),
+    ('numba', '0.52.0'),
+]
+
+download_dep_fail = True
+use_pip = True
+
+options = {'modulename': 'umap'}
+
+sanity_pip_check = True
+
+moduleclass = 'tools'

test/easyconfigs/easyconfigs.py

@@ -289,13 +289,14 @@ def check_dep_vars(self, gen, dep, dep_vars):
                 (r'5\.', [r'Elk-']),
             ],
             # some software depends on numba, which typically requires an older LLVM;
-            # this includes BirdNET, cryoDRGN, librosa, PyOD, Python-Geometric, scVelo, scanpy
+            # this includes BirdNET, cell2location, cryoDRGN, librosa, PyOD, Python-Geometric, scVelo, scanpy
             'LLVM': [
                 # numba 0.47.x requires LLVM 7.x or 8.x (see https://github.com/numba/llvmlite#compatibility)
                 (r'8\.', [r'numba-0\.47\.0-', r'librosa-0\.7\.2-', r'BirdNET-20201214-',
                           r'scVelo-0\.1\.24-', r'PyTorch-Geometric-1\.[34]\.2']),
-                (r'10\.0\.1', [r'cryoDRGN-0\.3\.2-', r'loompy-3\.0\.6-', r'numba-0\.52\.0-', r'PyOD-0\.8\.7-',
-                               r'PyTorch-Geometric-1\.6\.3', r'scanpy-1\.7\.2-']),
+                (r'10\.0\.1', [r'cell2location-0\.05-alpha-', r'cryoDRGN-0\.3\.2-', r'loompy-3\.0\.6-',
+                               r'numba-0\.52\.0-', r'PyOD-0\.8\.7-', r'PyTorch-Geometric-1\.6\.3',
+                               r'scanpy-1\.7\.2-', r'umap-learn-0\.4\.6-']),
             ],
             # rampart requires nodejs > 10, artic-ncov2019 requires rampart
             'nodejs': [('12.16.1', ['rampart-1.2.0rc3-', 'artic-ncov2019-2020.04.13'])],