#271 #278 progress #169 check #139 added

139_AMICA/AMICA.eb

@@ -0,0 +1,39 @@
+easyblock = 'CmdCp'
+
+name = 'AMICA'
+version = '2024.1.19'
+local_commit = 'e0db55f07c8c410641cd5b0df5498a5a53129ce6'
+
+homepage = 'https://github.com/sccn/amica'
+description = """Code for AMICA: Adaptive Mixture ICA with shared components"""
+
+toolchain = {'name': 'intel', 'version': '2023a'}
+toolchainopts = {'openmp': True}
+# https://github.com/sccn/amica/archive/e0db55f07c8c410641cd5b0df5498a5a53129ce6.zip
+source_urls = ['https://github.com/sccn/amica/archive/']
+# source_urls = ['https://github.com/sccn/amica/wiki/Amica-Download/27dc1d87dbb608ddccb3cf46202a179b3a943f0c/']
+sources = ['%s.zip' % local_commit]
+# sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] example
+checksums = ['5c581f0edaa7d7ae7a8a2a993db22c4d211b38860a20099b0b4e9a0dc5fa6162']
+
+# dependencies = [
+#     ('Python', '3.11.3'),
+#     ('Meson', '1.1.1'),
+#     ('Ninja', '1.11.1'),
+#     ('CMake', '3.26.3'),
+#     ('SAMtools', '1.18'),
+# ]
+
+# cmds_map = [('.*', "./compile")]
+install_cmd = "mpif90 -static-intel -fpp -O3 -march=core-avx2 -heap-arrays -qopenmp -mkl -DMKL -o amica15ex funmod2.f90 amica17.f90"
+test_cmd = "./amica17nsg ./amicadefs.param"
+files_to_copy = [(['install/bin/*'], 'bin'), (['install/lib/*'], 'lib'), (['install/include/*'], 'include')]
+
+# sanity_check_paths = {
+#     'files': ['bin/randseq', 'bin/indexlr', 'bin/mi_bf_generate'],
+#     'dirs': [],
+# }
+
+# sanity_check_commands = ['randseq --help', 'indexlr --help']
+
+moduleclass = 'math'

169_Bonito/Bonito2.eb

@@ -0,0 +1,59 @@
+# author: Denis Kristak (INUITS)
+easyblock = 'PythonBundle'
+
+name = 'Bonito'
+version = '0.7.1'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://github.com/nanoporetech/bonito'
+description = "Convolution Basecaller for Oxford Nanopore Reads"
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('CUDA', '11.7.0', '', SYSTEM),
+    ('SciPy-bundle', '2022.05'),
+    ('PyTorch', '1.12.1', '-CUDA-%(cudaver)s'),
+    ('edlib', '1.3.9'),
+    ('ont-fast5-api', '4.1.1'),
+]
+
+use_pip = True
+
+# strip out too strict version requirements for dependencies
+local_bonito_preinstallopts = "sed -i 's/[><=]=.*//g' requirements.txt && "
+# fix requirements for stuff we include as a proper dependency
+local_bonito_preinstallopts += "sed -i 's/genomeworks-cuda-10-2/genomeworks/g' requirements.txt && "
+local_bonito_preinstallopts += "sed -i 's/cupy-cuda102/cupy/g' requirements.txt && "
+local_bonito_preinstallopts += "sed -i 's/numpy~=[0-9.]*/numpy/g' requirements.txt && "
+local_bonito_preinstallopts += "sed -i 's/torch~=[0-9.]*/torch/g' requirements.txt && "
+local_bonito_preinstallopts += "export PATH=%(installdir)s/bin/:$PATH && "
+
+exts_list = [
+    ('fast-ctc-decode', '0.3.2', {
+        'source_tmpl': 'fast_ctc_decode-0.3.5-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl',
+        'unpack_sources': False,
+    }),
+    ('mappy', '2.24', {
+    }),
+    ('ont-bonito', version, {
+        'modulename': 'bonito',
+        'preinstallopts': local_bonito_preinstallopts,
+    }),
+]
+
+sanity_pip_check = True
+
+sanity_check_paths = {
+    'files': ['bin/bonito'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = [
+    "bonito --help",
+    "bonito convert --help",
+    "bonito download --help",
+]
+
+moduleclass = 'bio'

169_Bonito/old_Bonito-0.4.0-fosscuda-2020b.eb

@@ -0,0 +1,126 @@
+# author: Denis Kristak (INUITS)
+easyblock = 'PythonBundle'
+
+name = 'Bonito'
+version = '0.4.0'
+
+homepage = 'https://github.com/nanoporetech/bonito'
+description = "Convolution Basecaller for Oxford Nanopore Reads"
+
+toolchain = {'name': 'fosscuda', 'version': '2020b'}
+
+dependencies = [
+    ('Python', '3.8.6'),
+    ('SciPy-bundle', '2020.11'),
+    ('PyTorch', '1.7.1'),
+    ('h5py', '3.1.0'),
+    ('Mako', '1.1.3'),
+    ('PyYAML', '5.3.1'),
+    ('python-parasail', '1.2.4'),
+    ('tqdm', '4.56.2'),
+    ('apex', '20210420'),
+    ('minimap2', '2.18'),
+    ('CuPy', '8.5.0'),
+    ('GenomeWorks', '2021.02.2'),
+    ('pyspoa', '0.0.8'),
+    ('ont-fast5-api', '3.3.0'),
+]
+
+use_pip = True
+
+# strip out too strict version requirements for dependencies
+local_bonito_preinstallopts = "sed -i 's/[><=]=.*//g' requirements.txt && "
+# fix requirements for stuff we include as a proper dependency
+local_bonito_preinstallopts += "sed -i 's/genomeworks-cuda-10-2/genomeworks/g' requirements.txt && "
+local_bonito_preinstallopts += "sed -i 's/cupy-cuda102/cupy/g' requirements.txt && "
+local_bonito_preinstallopts += "sed -i 's/numpy~=[0-9.]*/numpy/g' requirements.txt && "
+local_bonito_preinstallopts += "sed -i 's/torch~=[0-9.]*/torch/g' requirements.txt && "
+local_bonito_preinstallopts += "export PATH=%(installdir)s/bin/:$PATH && "
+
+exts_list = [
+    ('python-editor', '1.0.4', {
+        'modulename': 'editor',
+        'checksums': ['51fda6bcc5ddbbb7063b2af7509e43bd84bfc32a4ff71349ec7847713882327b'],
+    }),
+    ('alembic', '1.6.4', {
+        'checksums': ['becb572c6701c90ca249f97fc1ae231468cc9516df367a350901eeb9310a8d43'],
+    }),
+    ('cmd2', '1.5.0', {
+        'checksums': ['701a8c9975c4abc45e5d13906ab149f959f812869106347323a3f89ac0e82a62'],
+    }),
+    ('prettytable', '2.1.0', {
+        'checksums': ['5882ed9092b391bb8f6e91f59bcdbd748924ff556bb7c634089d5519be87baa0'],
+    }),
+    ('cliff', '3.7.0', {
+        'preinstallopts': "sed -i'' 's/cmd2.*/cmd2/g' requirements.txt && ",
+        'checksums': ['389c81960de13f05daf1cbd546f33199e86c518ba4266c79ec7a153a280980ea'],
+    }),
+    ('colorlog', '5.0.1', {
+        'checksums': ['f17c013a06962b02f4449ee07cfdbe6b287df29efc2c9a1515b4a376f4e588ea'],
+    }),
+    ('greenlet', '1.1.0', {
+        'checksums': ['c87df8ae3f01ffb4483c796fe1b15232ce2b219f0b18126948616224d3f658ee'],
+    }),
+    ('SQLAlchemy', '1.4.15', {
+        'checksums': ['0ff100c75cd175f35f4d24375a0b3d82461f5b1af5fc8d112ef0e5ceea8049e6'],
+    }),
+    ('cmaes', '0.8.2', {
+        'checksums': ['1c04ba23ded925ef13b96f42cfbd667a905ea5b80754c750e6448b9fcda96a5d'],
+    }),
+    ('optuna', '2.7.0', {
+        'checksums': ['eb1595108ec444e840deb0037351074144fecb7a4eff6870fc11569ab782cfc6'],
+    }),
+    ('colorama', '0.4.4', {
+        'checksums': ['5941b2b48a20143d2267e95b1c2a7603ce057ee39fd88e7329b0c292aa16869b'],
+    }),
+    ('pyperclip', '1.8.2', {
+        'checksums': ['105254a8b04934f0bc84e9c24eb360a591aaf6535c9def5f29d92af107a9bf57'],
+    }),
+    ('importlib_metadata', '4.0.1', {
+        'checksums': ['8c501196e49fb9df5df43833bdb1e4328f64847763ec8a50703148b73784d581'],
+    }),
+    ('stevedore', '3.3.0', {
+        'checksums': ['3a5bbd0652bf552748871eaa73a4a8dc2899786bc497a2aa1fcb4dcdb0debeee'],
+    }),
+    ('fast-ctc-decode', '0.3.0', {
+        'source_tmpl': 'fast_ctc_decode-%(version)s-cp38-cp38-manylinux2010_x86_64.whl',
+        'unpack_sources': False,
+        'checksums': ['623d83f8de5e02199a09bfe0160a1e477f0db8d4ab612b26a7e42c2a335b378c'],
+    }),
+    ('mappy', '2.18', {
+        'checksums': ['18fffdb4b831cc3f5399b919b0942c640bf9a943ca22102ac446f53af3b905a8'],
+    }),
+    ('seqdist', '0.0.3', {
+        'preinstallopts': "sed -i 's/cupy-cuda102//g' settings.ini && sed -i 's/[<>=]=[0-9].*//g' settings.ini && ",
+        'checksums': ['bdbbea6ebba1c6dd6698d46e23ba7858f93a7cdf0c7cbc2ea66660291acb044f'],
+    }),
+    ('crf-beam', '0.0.1a0', {
+        'modulename': 'kbeam',
+        'sources': ['crf_beam-%(version)s-cp38-cp38-manylinux1_x86_64.whl'],
+        'unpack_sources': False,
+        'checksums': ['0cba80ff4d7f90595f498921cf904736e3bce558dba80de5611874d89e72312e'],
+    }),
+    ('networkx', '2.5.1', {
+        'checksums': ['109cd585cac41297f71103c3c42ac6ef7379f29788eb54cb751be5a663bb235a'],
+    }),
+    ('ont-bonito', version, {
+        'modulename': 'bonito',
+        'preinstallopts': local_bonito_preinstallopts,
+        'checksums': ['429310d56e2d7dabd91a9a9c972504a0aa2b6d6469563b14d4aae30adfe9a87e'],
+    }),
+]
+
+sanity_pip_check = True
+
+sanity_check_paths = {
+    'files': ['bin/bonito'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = [
+    "bonito --help",
+    "bonito convert --help",
+    "bonito download --help",
+]
+
+moduleclass = 'bio'

271_phyluce/phyluce-1.7.3-foss-2023a.eb

@@ -48,16 +48,18 @@ exts_list = [
             '%(name)s-%(version)s_removal-Bio-Alphabet.patch',
         ],
         'checksums': [
-            '931fd512730bb101266b27728576df00277858d256e1ab30d64b474588362e11',     # v1.7.3.tar.gz
-            '543daee90e1422a7a43c304d6f33e5f16411cc7b85c522b847388feff8cc402a',           # phyluce-1.7.3_fix-config-paths.patch
-            'f6c5237552fde5a3bf24105781a9001ee5e87bbd825015fc1aa6b5c6a147e171',        # phyluce-1.7.3_removal-Bio-Alphabet.patch
+            # v1.7.3.tar.gz
+            '931fd512730bb101266b27728576df00277858d256e1ab30d64b474588362e11',
+            # phyluce-1.7.3_fix-config-paths.patch
+            '543daee90e1422a7a43c304d6f33e5f16411cc7b85c522b847388feff8cc402a',
+            # phyluce-1.7.3_removal-Bio-Alphabet.patch
+            'f6c5237552fde5a3bf24105781a9001ee5e87bbd825015fc1aa6b5c6a147e171',
         ],
     }),
 ]
 
 use_pip = True
 sanity_pip_check = True
-download_dep_fail = True
 
 sanity_check_paths = {
     'files': [],

278_FFAVES/FFAVES.eb

@@ -41,9 +41,9 @@ exts_list = [
     }),
 ]
 
-# sanity_check_paths = {
-#     'files': ['bin/%s' % x for x in ['ffaves.py', 'get_gprof', 'get_objgraph', 'undill']],
-#     'dirs': ['lib/python%(pyshortver)s/site-packages/'],
-# }
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in ['ffaves.py', 'get_gprof', 'get_objgraph', 'undill']],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/'],
+}
 
 moduleclass = 'bio'