#305 CPLEX debuging

305_compass/CPLEX-11.3.0.eb

@@ -0,0 +1,26 @@
+name = 'CPLEX'
+version = '22.1.1'
+
+homepage = 'https://www.ibm.com/analytics/cplex-optimizer'
+description = """IBM ILOG CPLEX Optimizer's mathematical programming technology enables
+ analytical decision support for improving efficiency,
+ reducing costs, and increasing profitability."""
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+# cplex_studio2211.linux_x86_64.bin
+sources = ['cplex_studio%s.linux_x86_64.bin' % ''.join(version.split('.'))]
+checksums = ['ab6d3f0953fdb3cbd43854452357955ef96db8b751c0866de3572fc47a0df542']
+
+download_instructions = """
+1. Visit https://www.ibm.com/products/ilog-cplex-optimization-studio
+2. Sign up and download the Academic Edition
+"""
+
+builddependencies = [('binutils', '2.38')]
+
+dependencies = [
+    ('Java', '11', '', SYSTEM),
+    ('Python', '3.10.4'),
+]
+
+moduleclass = 'math'

305_compass/CPLEX-12.3.0.eb

@@ -0,0 +1,27 @@
+name = 'CPLEX'
+version = '22.1.1'
+
+homepage = 'https://www.ibm.com/analytics/cplex-optimizer'
+description = """IBM ILOG CPLEX Optimizer's mathematical programming technology enables
+ analytical decision support for improving efficiency,
+ reducing costs, and increasing profitability."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+# cplex_studio2211.linux_x86_64.bin
+sources = ['cplex_studio%s.linux_x86_64.bin' % ''.join(version.split('.'))]
+checksums = ['ab6d3f0953fdb3cbd43854452357955ef96db8b751c0866de3572fc47a0df542']
+
+download_instructions = """
+1. Visit https://www.ibm.com/products/ilog-cplex-optimization-studio
+2. Sign up and download the Academic Edition
+"""
+
+builddependencies = [('binutils', '2.40')]
+
+dependencies = [
+    ('Java', '11', '', SYSTEM),
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),
+]
+
+moduleclass = 'math'

305_compass/compass-foss-2022a.eb

@@ -0,0 +1,42 @@
+easyblock = 'PythonBundle'
+
+name = 'Compass'
+version = '2024.04'
+
+homepage = 'https://github.com/YosefLab/Compass'
+description = """In-Silico Modeling of Metabolic Heterogeneity using Single-Cell Transcriptomes."""
+local_commit = "7664cb0"
+
+toolchain = {'name': 'foss', 'version': '2022a'} # 11.3.0
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'), 
+    ('tqdm', '4.64.0'),
+    ('python-libsbml', '5.20.2'),
+    ('scikit-learn', '1.1.2'),
+    ('python-igraph', '0.10.3'),
+    ('leidenalg', '0.9.1'),
+    ('anndata', '0.8.0'),
+    ('CPLEX', '22.1.1', '', SYSTEM),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('compass', version, {
+        # delete dependecy python-igraph - pip check failing
+        'preinstallopts': "sed -i '27d' setup.py && ",
+        'source_urls': ['https://github.com/YosefLab/Compass/archive/'],
+        'sources': [{
+            'download_filename': '%s.tar.gz' % local_commit,
+            'filename': '%%(name)s-%%(version)s-%s.tar.gz' % local_commit,
+        }],
+        'checksums': ['87529c5fae108fa2a8e3e35438d3b25874faa78af670a2349228c76fa0843376'],
+    }),
+]
+
+# sanity_check_commands = ["python -c 'import igraph'", "compass -h", "python -c 'import cplex'"]
+
+moduleclass = 'bio'

305_compass/compass-foss-2022b.eb

@@ -0,0 +1,42 @@
+easyblock = 'PythonBundle'
+
+name = 'Compass'
+version = '2024.04'
+
+homepage = 'https://github.com/YosefLab/Compass'
+description = """In-Silico Modeling of Metabolic Heterogeneity using Single-Cell Transcriptomes."""
+local_commit = "7664cb0"
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('SciPy-bundle', '2023.02'), 
+    ('tqdm', '4.64.1'),
+    # ('python-libsbml', '5.20.2'), NOT in EB (only 2021a)
+    ('scikit-learn', '1.2.1'),
+    ('python-igraph', '0.10.6'),
+    ('leidenalg', '0.10.1'),
+    # ('anndata', '0.10.5.post1'), NOT in EB (only 2022a)
+    ('CPLEX', '22.1.1', '', SYSTEM),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('compass', version, {
+        # delete dependecy python-igraph - pip check failing
+        'preinstallopts': "sed -i '27d' setup.py && ",
+        'source_urls': ['https://github.com/YosefLab/Compass/archive/'],
+        'sources': [{
+            'download_filename': '%s.tar.gz' % local_commit,
+            'filename': '%%(name)s-%%(version)s-%s.tar.gz' % local_commit,
+        }],
+        'checksums': ['87529c5fae108fa2a8e3e35438d3b25874faa78af670a2349228c76fa0843376'],
+    }),
+]
+
+sanity_check_commands = ["python -c 'import igraph'", "compass -h", "python -c 'import cplex'"]
+
+moduleclass = 'bio'

305_compass/compass.eb

@@ -9,56 +9,35 @@ local_commit = "7664cb0"
 
 toolchain = {'name': 'foss', 'version': '2023a'}
 
-# builddependencies = [
-#     ('CMake', '3.26.3'),
-#     ('poetry', '1.5.1'),
-# ]
-
-# 'numpy>=1.12', OK scipy bundle
-# 'pandas>=0.20', OK scipy bundle
-# 'tqdm>=4.11', OK deps
-# 'python-libsbml>=5.13', OK created
-# 'six>=1.10', OK pybundle (1.16)
-# 'scikit-learn>=0.19', OK deps
-# 'scipy>=1.0', OK scipy bundle
-# 'python-igraph>=0.9', OK deps
-# 'leidenalg>=0.8.2', OK deps
-# 'anndata' OK deps
-
 dependencies = [
     ('Python', '3.11.3'),
-    ('Python-bundle-PyPI', '2023.06'),  # six
+    ('Python-bundle-PyPI', '2023.06'),
     ('SciPy-bundle', '2023.07'),
-    # ('CPLEX', '22.1.1', '', SYSTEM),
     ('tqdm', '4.66.1'),
     ('python-libsbml', '5.20.2'),
     ('scikit-learn', '1.3.1'),
     ('python-igraph', '0.11.4'),
     ('leidenalg', '0.10.2'),
     ('anndata', '0.10.5.post1'),
+    ('CPLEX', '22.1.1', '', SYSTEM),
 ]
 
 use_pip = True
 sanity_pip_check = True
 
 exts_list = [
     ('compass', version, {
+        # delete dependecy python-igraph - pip check failing
         'preinstallopts': "sed -i '27d' setup.py && ",
         'source_urls': ['https://github.com/YosefLab/Compass/archive/'],
-        'sources': [{'download_filename': '7664cb0.tar.gz', 'filename': '%(name)s-%(version)s-7664cb0.tar.gz'}],
+        'sources': [{
+            'download_filename': '%s.tar.gz' % local_commit,
+            'filename': '%%(name)s-%%(version)s-%s.tar.gz' % local_commit,
+        }],
         'checksums': ['87529c5fae108fa2a8e3e35438d3b25874faa78af670a2349228c76fa0843376'],
     }),
 ]
 
-# exts_list = [
-#     ('compass', version, {
-#         'source_urls': ['https://github.com/YosefLab/Compass/archive/'],
-#         'sources': [{
-#             'download_filename': '%s.tar.gz' % local_commit,
-#             'filename': '%%(name)s-%%(version)s-%s.tar.gz' % local_commit,
-#         }],
-#         'checksums': ['87529c5fae108fa2a8e3e35438d3b25874faa78af670a2349228c76fa0843376'],
-#     }),
-# ]
+sanity_check_commands = ["python -c 'import igraph'", "compass -h", "python -c 'import cplex'"]
 
 moduleclass = 'bio'

305_compass/python-libsbml-2022a.eb

@@ -0,0 +1,44 @@
+# This is a contribution from SIB Swiss Institute of Bioinformatics
+# Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it
+# Authors: Sebastien Moretti <[email protected]>
+# Update: Pavel Tománek (INUITS)
+
+easyblock = 'PythonBundle'
+
+name = 'python-libsbml'
+version = '5.20.2'
+
+homepage = 'https://sbml.org/'
+description = """LibSBML Python API."""
+
+toolchain = {'name': 'foss', 'version': '2022a'} # 11.3.0
+
+builddependencies = [
+    ('binutils', '2.38'),
+    ('CMake', '3.23.1'),
+    ('make', '4.3'),
+    ('Check', '0.15.2'),
+    ('SWIG', '4.0.2'),
+    ('expat', '2.4.8'),
+    ('bzip2', '1.0.8'),
+    ('zlib', '1.2.12'),
+]
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('libxml2', '2.9.13'),
+    ('libxslt', '1.1.34'),
+]
+
+use_pip = True
+
+exts_list = [
+    (name, version, {
+        'modulename': 'libsbml',
+        'checksums': ['0af5cbff68c9b52bac4bd7bb261f93a60832dc8cb31dafc90d3aff51467935b7'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'