progress #331 #336

vscentrum · May 17, 2024 · aaa6ef6 · aaa6ef6
1 parent 0da648b
commit aaa6ef6
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Showing 5 changed files with 107 additions and 62 deletions.
diff --git a/331_CellBender/CellBender_cpu.eb b/331_CellBender/CellBender_cpu.eb
@@ -27,61 +27,10 @@ dependencies = [
 
 use_pip = True
 
-local_comm_preinstallopts = """sed -i -e 's/^requires.*hatchling.*/requires = ["setuptools"]/g' """
-local_comm_preinstallopts += """-e 's/^build-backend.*/build-backend = "setuptools.build_meta"/g' """
-local_comm_preinstallopts += """-e 's/^dynamic = .*version.*/version = "%(version)s"/g' pyproject.toml && """
-
-#  cellbender 0.3.0 requires jupyter, which is not installed.
-#  cellbender 0.3.0 has requirement nbconvert<7.0.0, but you have nbconvert 7.7.4.
-#  cellbender 0.3.0 has requirement notebook<7.0.0, but you have notebook 7.0.2.
-
-# jupyter 1.0.0 requires jupyter-console, which is not installed.
-# cellbender 0.3.0 has requirement nbconvert<7.0.0, but you have nbconvert 7.7.4.
-# cellbender 0.3.0 has requirement notebook<7.0.0, but you have notebook 7.0.2.
-
-# cellbender 0.3.0 has requirement nbconvert<7.0.0, but you have nbconvert 7.7.4.
-# cellbender 0.3.0 has requirement notebook<7.0.0, but you have notebook 7.0.2.
-
-# nbconvert 6.5.4 has requirement mistune<2,>=0.8.1, but you have mistune 3.0.1.
-
-# exts_list = [ #update this
-#     ('setuptools', '69.0.3', {
-#         'checksums': ['be1af57fc409f93647f2e8e4573a142ed38724b8cdd389706a867bb4efcf1e78'],
-#     }),
-#     ('comm', '0.2.1', {
-#         'checksums': ['0bc91edae1344d39d3661dcbc36937181fdaddb304790458f8b044dbc064b89a'],
-#         'preinstallopts': local_comm_preinstallopts,
-#     }),
-#     # jupyter-console 6.6.3 requires ipykernel>=6.14
-#     ('ipykernel', '6.20.2', {
-#         'source_tmpl': SOURCE_PY3_WHL,
-#         'checksums': ['5d0675d5f48bf6a95fd517d7b70bcb3b2c5631b2069949b5c2d6e1d7477fb5a0'],
-#     }),
-#     # jupyter-console 6.6.3 requires jupyter-core!=5.0.*,>=4.12
-#     ('jupyter_core', '4.12.0', {
-#         'source_tmpl': SOURCE_PY3_WHL,
-#         'checksums': ['a54672c539333258495579f6964144924e0aa7b07f7069947bef76d7ea5cb4c1'],
-#     }),
-    # # jupyter-console 6.6.3 requires traitlets>=5.4
-    # ('traitlets', '5.14.1', {
-    #     'source_tmpl': SOURCE_PY3_WHL,
-    #     'checksums': ['2e5a030e6eff91737c643231bfcf04a65b0132078dad75e4936700b213652e74'],
-    # }),
-    # ('jupyter_console', '6.6.3', {
-    #     'source_tmpl': SOURCE_PY3_WHL,
-    #     'checksums': ['309d33409fcc92ffdad25f0bcdf9a4a9daa61b6f341177570fdac03de5352485'],
-    # }),
-    # ('jupyter', '1.0.0', {
-    #     'checksums': ['d9dc4b3318f310e34c82951ea5d6683f67bed7def4b259fafbfe4f1beb1d8e5f'],
-    # }),
-#     ('cellbender', version, {
-#         #'source_urls': ['https://github.com/broadinstitute/CellBender/archive'],
-#         #'sources': [{'download_filename': '%s.tar.gz' % local_commit, 'filename': '%(name)s-%(version)s.tar.gz'}],
-#         #'checksums': ['7eb67837d28495adb82147e80a2ab58eeb406c5d91aa69dd0cc120d9cb3d6396'],
-#     }),
-# ]
-
 exts_list = [
+    ('async-timeout', '4.0.3', {
+        'checksums': ['4640d96be84d82d02ed59ea2b7105a0f7b33abe8703703cd0ab0bf87c427522f'],
+    }),
     ('traitlets', '5.14.1', {
         'source_tmpl': SOURCE_PY3_WHL,
         'checksums': ['2e5a030e6eff91737c643231bfcf04a65b0132078dad75e4936700b213652e74'],
@@ -100,7 +49,7 @@ exts_list = [
         'checksums': ['59a3429db53c50b5c6bcc8a07f8848cb00d7dc8bdb431a4ab41920d201d4756e'],
     }),
     ('nbconvert', '6.5.4', {
-        'checksums': ['9e3c7c6d491374cbdd5f35d268c05809357716d346f4573186bbeab32ee50bc1'],    
+        'checksums': ['9e3c7c6d491374cbdd5f35d268c05809357716d346f4573186bbeab32ee50bc1'],
     }),
     ('cellbender', version, {
         'checksums': ['94a46fb2b5921414ea86213cfdebca267b9ba6ba02df854cbd353980ab3aff42'],

diff --git a/331_CellBender/CellBender_gpu.eb b/331_CellBender/CellBender_gpu.eb
@@ -0,0 +1,72 @@
+easyblock = 'PythonBundle'
+
+name = 'CellBender'
+version = '0.3.0'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'http://github.com/broadinstitute/CellBender'
+description = """
+CellBender is a software package for eliminating technical artifacts from
+high-throughput single-cell RNA sequencing (scRNA-seq) data.
+"""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('CUDA', '12.1.1', '', SYSTEM),
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('matplotlib', '3.7.2'),
+    ('PyTorch', '2.1.2', versionsuffix),
+    ('IPython', '8.14.0'),
+    ('anndata', '0.10.5.post1'),
+    ('jupyter-contrib-nbextensions', '0.7.0'),
+    ('pyro-ppl', '1.9.0', versionsuffix),
+    ('loompy', '3.0.7'),
+    ('PyTables', '3.8.0'),
+    ('Qtconsole', '5.5.1'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('async-timeout', '4.0.3', {
+        'checksums': ['4640d96be84d82d02ed59ea2b7105a0f7b33abe8703703cd0ab0bf87c427522f'],
+    }),
+    ('traitlets', '5.14.1', {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['2e5a030e6eff91737c643231bfcf04a65b0132078dad75e4936700b213652e74'],
+    }),
+    ('jupyter_console', '6.6.3', {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['309d33409fcc92ffdad25f0bcdf9a4a9daa61b6f341177570fdac03de5352485'],
+    }),
+    ('jupyter', '1.0.0', {
+        'checksums': ['d9dc4b3318f310e34c82951ea5d6683f67bed7def4b259fafbfe4f1beb1d8e5f'],
+    }),
+    ('notebook', '6.5.7', {
+        'checksums': ['04eb9011dfac634fbd4442adaf0a8c27cd26beef831fe1d19faf930c327768e4'],
+    }),
+    ('mistune', '0.8.4', {
+        'checksums': ['59a3429db53c50b5c6bcc8a07f8848cb00d7dc8bdb431a4ab41920d201d4756e'],
+    }),
+    ('nbconvert', '6.5.4', {
+        'checksums': ['9e3c7c6d491374cbdd5f35d268c05809357716d346f4573186bbeab32ee50bc1'],
+    }),
+    ('cellbender', version, {
+        'checksums': ['94a46fb2b5921414ea86213cfdebca267b9ba6ba02df854cbd353980ab3aff42'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/cellbender'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = [
+    "cellbender --help",
+]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'
diff --git a/331_CellBender/pyro-ppl_cpu.eb b/331_CellBender/pyro-ppl_cpu.eb
@@ -30,6 +30,7 @@ exts_list = [
     }),
     (name, version, {
         'modulename': 'pyro',
+        'checksums': ['41f4c005159568280fbc511648960a98a2b1a410027d8bd0a43220ac9b102cdf'],
     }),
 ]
 

diff --git a/331_CellBender/pyro-ppl_gpu.eb b/331_CellBender/pyro-ppl_gpu.eb
@@ -32,6 +32,7 @@ exts_list = [
     }),
     (name, version, {
         'modulename': 'pyro',
+        'checksums': ['41f4c005159568280fbc511648960a98a2b1a410027d8bd0a43220ac9b102cdf'],
     }),
 ]
 

diff --git a/336_Atropos/atropos.eb b/336_Atropos/atropos.eb
@@ -11,7 +11,7 @@ toolchain = {'name': 'GCC', 'version': '12.3.0'}
 dependencies = [
     ('Python', '3.11.3'),
     ('Python-bundle-PyPI', '2023.06'),
-    # ('SciPy-bundle', '2023.07'),
+    # ('SciPy-bundle', '2023.07'), # only for versioneer
     ('tqdm', '4.66.1'),
     ('Pysam', '0.22.0'),
     ('pytest', '7.4.2'),
@@ -20,15 +20,37 @@ dependencies = [
 use_pip = True
 sanity_pip_check = True
 
+# srastream 0.1.3 requires xphyle, which is not installed. OK
+# khmer 2.1.1 requires bz2file, which is not installed. OK
+# khmer 2.1.1 requires screed, which is not installed. OK
+# xphyle 4.0.5 requires pokrok, which is not installed. OK
+# ModuleNotFoundError: No module named 'ngs'
+
 exts_list = [
-  ('versioneer', '0.29', {
+    ('versioneer', '0.29', {
         'checksums': ['5ab283b9857211d61b53318b7c792cf68e798e765ee17c27ade9f6c924235731'],
-  }),
-  ('khmer', '2.1.1', {
+    }),
+    ('screed', '1.1.3', {
+        'checksums': ['37e81697c7dba95a053554e5b5a86aff329705e1cf5dfc5e7b8da586dee072b8'],
+    }),
+    ('bz2file', '0.98', {
+        'checksums': ['64c1f811e31556ba9931953c8ec7b397488726c63e09a4c67004f43bdd28da88'],
+    }),
+    ('khmer', '2.1.1', {
         'checksums': ['a709606910bb8679bd8525e9d2bf6d1421996272e343b54cc18090feb2fdbe24'],
-  }),
-  ('srastream', '0.1.3'),
-  (name, version),
+    }),
+    # ('pokrok', '0.2.0', {
+    #     'checksums': ['cfe7956602d8bbc142a07bcb259e0d1d939f96d7b074e00dceea3cb5e39244e8'],
+    # }),
+    # ('xphyle', '4.0.5', {
+    #     'checksums': ['b744723a3c88d81318c7291c32682b8715a046f70d0a1db729bda783fd5e08bd'],
+    # }),
+    # ('srastream', '0.1.3', {
+    #     'checksums': ['7f2cfd76ae988349ad5407a952cd4c133ae5dff7cf12c76072c53d82b50c2634'],
+    # }),
+    (name, version, {
+        'checksums': ['17e9dc3d76d7a2ca607a12da191a6d7ba1cfbd1a8c924215870417f85858fd83'],
+    }),
 ]
 
 sanity_check_paths = {
-Original file line number
+Diff line change
@@ Expand Up / @@ -30,6 +30,7 @@ exts_list = [ @@
         }),
         (name, version, {
             'modulename': 'pyro',
+            'checksums': ['41f4c005159568280fbc511648960a98a2b1a410027d8bd0a43220ac9b102cdf'],
         }),
     ]
@@ Expand Down @@