#278 progress

278_FFAVES/FFAVES.eb

@@ -10,66 +10,40 @@ Use FFAVES to amplify the signal of groups of co-regulating genes in an unsuperv
 By amplifying the signal of genes with correlated expression, while filtering out genes that are randomly expressed,
 we can identify a subset of genes more predictive of different cell types.
 The output of FFAVES can then be used in our second algorithm, entropy sort feature weighting (ESFW),
-to create a ranked list of genes that are most likely to pertain to distinct sub-populations of cells in an scRNA-seq dataset.
+to create a ranked list of genes that are most likely to pertain to distinct 
+sub-populations of cells in an scRNA-seq dataset.
 """
 
 toolchain = {'name': 'foss', 'version': '2022a'}
-# toolchainopts = {'openmp': True}
-
-# builddependencies = [('Python', '3.10.4'),]
 
 dependencies = [
     ('Python', '3.10.4'),
     ('SciPy-bundle', '2022.05'),
-#     ('h5py', '3.7.0'),
-#     ('networkx', '2.8.4'),
-#     ('numba', '0.56.4'),
-#     ('PyTables', '3.8.0'),
-#     ('statsmodels', '0.13.1'),
-#     ('scikit-learn', '1.1.2'),
-#     ('Seaborn', '0.12.1'),
-#     ('tqdm', '4.64.0'),
-#     ('leidenalg', '0.9.1'),
-#     ('umap-learn', '0.5.3'),
 ]
 
 use_pip = True
 sanity_pip_check = True
 
-# prebuildopts = "ls -lh && cd %(name)s-%(version)s && sed -i 's/==/>=/' requirements.txt && echo 'AAABBB' && cat requirements.txt && ls -lh && "
-# preinstallopts = "ls -lh && cd %(name)s-%(version)s && sed -i 's/==/>=/' requirements.txt && echo 'AAABBB' && cat requirements.txt && ls -lh && "
-
 exts_list = [
     ('dill', '0.3.8', {
         'checksums': ['3ebe3c479ad625c4553aca177444d89b486b1d84982eeacded644afc0cf797ca'],
     }),
-    # ('numpy', '1.20.3', {
-    #     'source_tmpl': 'numpy-%(version)s.zip',
-    #     'checksums': ['e55185e51b18d788e49fe8305fd73ef4470596b33fc2c1ceb304566b99c71a69'],
-    # }),
-    # ('scipy', '1.7.3', {
-    #     'checksums': ['ab5875facfdef77e0a47d5fd39ea178b58e60e454a4c85aa1e52fcb80db7babf'],
-    # }),
     ('multiprocess', '0.70.12.2', {
         'source_tmpl': 'multiprocess-%(version)s.zip',
         'checksums': ['206bb9b97b73f87fec1ed15a19f8762950256aa84225450abc7150d02855a083'],
     }),
     (name, version, {
         'source_urls': ['https://github.com/aradley/FFAVES/archive/'],
         'sources': [{'download_filename': '2c1fa89.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
-        'preinstallopts': "sed -i 's/==/>=/' requirements.txt && ",
+        # numpy and scipy requirements are too strict, it can not be combinated with toolchain and SciPy-bundle
+        'preinstallopts': "sed -i 's/numpy==/numpy>=/;s/scipy==/scipy>=/' requirements.txt && ",
         'checksums': ['b833cc26cc60ad44c48d1b5712ce32b0ceb7f8d7876c06466514f79d357e4f83'],
     }),
 ]
 
 # sanity_check_paths = {
-#     'files': ['bin/%s' % x for x in ['natsort', 'scanpy']],
+#     'files': ['bin/%s' % x for x in ['ffaves.py', 'get_gprof', 'get_objgraph', 'undill']],
 #     'dirs': ['lib/python%(pyshortver)s/site-packages/'],
 # }
 
-# sanity_check_commands = [
-#     "natsort --help",
-#     "scanpy --help",
-# ]
-
 moduleclass = 'bio'