diff --git a/331_CellBender/CellBender_cpu.eb b/331_CellBender/CellBender_cpu.eb index d61e3e94..5fb9920f 100644 --- 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 new file mode 100644 index 00000000..94c6fc2c --- /dev/null +++ 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 index 6f74e489..28ed959d 100644 --- 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 index 2ae2f8b9..4add431b 100644 --- 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 index 38b289c4..5994710e 100644 --- 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 = {