Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

{bio}[foss/2023a] Bonito v0.8.1, ont-remora v3.3.0 w/ CUDA 12.1.1 #21979

Merged
merged 1 commit into from
Dec 20, 2024
Merged

{bio}[foss/2023a] Bonito v0.8.1, ont-remora v3.3.0 w/ CUDA 12.1.1 #21979

merged 1 commit into from
Dec 20, 2024

Conversation

pavelToman
Copy link
Collaborator

@pavelToman pavelToman commented Dec 5, 2024 •
edited
Loading

(created using eb --new-pr)
resolves vscentrum/vsc-software-stack#169

@github-actions GitHub Actions
Copy link

github-actions bot commented Dec 5, 2024

Updated software Bonito-0.8.1-foss-2023a-CUDA-12.1.1.eb

Diff against Bonito-0.4.0-fosscuda-2020b.eb

easybuild/easyconfigs/b/Bonito/Bonito-0.4.0-fosscuda-2020b.eb

diff --git a/easybuild/easyconfigs/b/Bonito/Bonito-0.4.0-fosscuda-2020b.eb b/easybuild/easyconfigs/b/Bonito/Bonito-0.8.1-foss-2023a-CUDA-12.1.1.eb
index 59554e81a1..83cbc16113 100644
--- a/easybuild/easyconfigs/b/Bonito/Bonito-0.4.0-fosscuda-2020b.eb
+++ b/easybuild/easyconfigs/b/Bonito/Bonito-0.8.1-foss-2023a-CUDA-12.1.1.eb
@@ -1,112 +1,48 @@
-# author: Denis Kristak (INUITS)
 easyblock = 'PythonBundle'
 
 name = 'Bonito'
-version = '0.4.0'
+version = '0.8.1'
+versionsuffix = '-CUDA-%(cudaver)s'
 
 homepage = 'https://github.com/nanoporetech/bonito'
 description = "Convolution Basecaller for Oxford Nanopore Reads"
 
-toolchain = {'name': 'fosscuda', 'version': '2020b'}
+toolchain = {'name': 'foss', 'version': '2023a'}
 
 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'),
+    ('CUDA', '12.1.1', '', SYSTEM),
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('SciPy-bundle', '2023.07'),
+    ('PyTorch', '2.1.2', versionsuffix),
+    ('edlib', '1.3.9'),
+    ('ont-fast5-api', '4.1.2'),
+    ('ont-remora', '3.3.0', versionsuffix),
+    ('python-parasail', '1.3.4'),
+    ('pod5-file-format', '0.3.10'),
+    ('Pysam', '0.22.0'),
+    ('tqdm', '4.66.1'),
 ]
 
 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 = [
-    ('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',
+    ('fast-ctc-decode', '0.3.6', {
+        'source_tmpl': 'fast_ctc_decode-0.3.6-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl',
         'unpack_sources': False,
-        'checksums': ['623d83f8de5e02199a09bfe0160a1e477f0db8d4ab612b26a7e42c2a335b378c'],
-    }),
-    ('mappy', '2.18', {
-        'checksums': ['18fffdb4b831cc3f5399b919b0942c640bf9a943ca22102ac446f53af3b905a8'],
+        'checksums': ['f49994a475866edf0e61f0d9e1b41185c035ba559b8c2aa68f83342d2c80ee6b'],
     }),
-    ('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'],
+    ('mappy', '2.28', {
+        'checksums': ['0ebf7a5d62bd668f5456028215e26176e180ca68161ac18d4f7b48045484cebb'],
     }),
-    ('networkx', '2.5.1', {
-        'checksums': ['109cd585cac41297f71103c3c42ac6ef7379f29788eb54cb751be5a663bb235a'],
+    ('ont_koi', '0.4.4', {
+        'source_tmpl': 'ont_koi-0.4.4-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl',
+        'modulename': 'koi',
+        'checksums': ['e5d7c93b26363a3d4e3778f972d1f149447adbde91925e8876a97e7a63774e28'],
     }),
     ('ont-bonito', version, {
         'modulename': 'bonito',
-        'preinstallopts': local_bonito_preinstallopts,
-        'checksums': ['429310d56e2d7dabd91a9a9c972504a0aa2b6d6469563b14d4aae30adfe9a87e'],
+        'checksums': ['26df86ee233bf020b549177e1e2aaa7ad7d99cf0927d79ab3fa31c1670d09ba6'],
     }),
 ]
 
@@ -119,7 +55,6 @@ sanity_check_paths = {
 
 sanity_check_commands = [
     "bonito --help",
-    "bonito convert --help",
     "bonito download --help",
 ]
Diff against Bonito-0.3.8-fosscuda-2020b.eb

easybuild/easyconfigs/b/Bonito/Bonito-0.3.8-fosscuda-2020b.eb

diff --git a/easybuild/easyconfigs/b/Bonito/Bonito-0.3.8-fosscuda-2020b.eb b/easybuild/easyconfigs/b/Bonito/Bonito-0.8.1-foss-2023a-CUDA-12.1.1.eb
index b677ee8f20..83cbc16113 100644
--- a/easybuild/easyconfigs/b/Bonito/Bonito-0.3.8-fosscuda-2020b.eb
+++ b/easybuild/easyconfigs/b/Bonito/Bonito-0.8.1-foss-2023a-CUDA-12.1.1.eb
@@ -1,103 +1,48 @@
 easyblock = 'PythonBundle'
 
 name = 'Bonito'
-version = '0.3.8'
+version = '0.8.1'
+versionsuffix = '-CUDA-%(cudaver)s'
 
 homepage = 'https://github.com/nanoporetech/bonito'
 description = "Convolution Basecaller for Oxford Nanopore Reads"
 
-toolchain = {'name': 'fosscuda', 'version': '2020b'}
+toolchain = {'name': 'foss', 'version': '2023a'}
 
 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'),
+    ('CUDA', '12.1.1', '', SYSTEM),
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('SciPy-bundle', '2023.07'),
+    ('PyTorch', '2.1.2', versionsuffix),
+    ('edlib', '1.3.9'),
+    ('ont-fast5-api', '4.1.2'),
+    ('ont-remora', '3.3.0', versionsuffix),
+    ('python-parasail', '1.3.4'),
+    ('pod5-file-format', '0.3.10'),
+    ('Pysam', '0.22.0'),
+    ('tqdm', '4.66.1'),
 ]
 
 use_pip = True
 
 exts_list = [
-    ('python-editor', '1.0.4', {
-        'modulename': 'editor',
-        'checksums': ['51fda6bcc5ddbbb7063b2af7509e43bd84bfc32a4ff71349ec7847713882327b'],
-    }),
-    ('alembic', '1.5.8', {
-        'checksums': ['e27fd67732c97a1c370c33169ef4578cf96436fa0e7dcfaeeef4a917d0737d56'],
-    }),
-    ('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', '1.0.0', {
-        'checksums': ['719e169c79255816cdcf6dccd9ed2d089a72a9f6c42273aae12d55e8d35bdcf8'],
-    }),
-    ('SQLAlchemy', '1.4.11', {
-        'checksums': ['4ad4044eb86fbcbdff2106e44f479fbdac703d77860b3e19988c8a8786e73061'],
-    }),
-    ('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'],
-    }),
-    ('progressbar33', '2.4', {
-        'modulename': 'progressbar',
-        'checksums': ['51fe0d9b3b4023db2f983eeccdfc8c9846b84db8443b9bee002c7f58f4376eff'],
-    }),
-    ('ont-fast5-api', '3.3.0', {
-        'checksums': ['8ccbf8d203ba90c2757f25b6bbcfb0e5c90bbbb9972f2e19c3f6d6d9943d9f15'],
-    }),
-    ('fast-ctc-decode', '0.3.0', {
-        'source_tmpl': 'fast_ctc_decode-%(version)s-cp38-cp38-manylinux2010_x86_64.whl',
+    ('fast-ctc-decode', '0.3.6', {
+        'source_tmpl': 'fast_ctc_decode-0.3.6-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl',
         'unpack_sources': False,
-        'checksums': ['623d83f8de5e02199a09bfe0160a1e477f0db8d4ab612b26a7e42c2a335b378c'],
+        'checksums': ['f49994a475866edf0e61f0d9e1b41185c035ba559b8c2aa68f83342d2c80ee6b'],
     }),
-    ('mappy', '2.18', {
-        'checksums': ['18fffdb4b831cc3f5399b919b0942c640bf9a943ca22102ac446f53af3b905a8'],
+    ('mappy', '2.28', {
+        'checksums': ['0ebf7a5d62bd668f5456028215e26176e180ca68161ac18d4f7b48045484cebb'],
     }),
-    ('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'],
+    ('ont_koi', '0.4.4', {
+        'source_tmpl': 'ont_koi-0.4.4-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl',
+        'modulename': 'koi',
+        'checksums': ['e5d7c93b26363a3d4e3778f972d1f149447adbde91925e8876a97e7a63774e28'],
     }),
     ('ont-bonito', version, {
         'modulename': 'bonito',
-        'preinstallopts': "sed -i 's/[><=]=.*//g' requirements.txt && export PATH=%(installdir)s/bin:$PATH && ",
-        'checksums': ['f18ec073c841bb0ccfe9049530df370ab0fb19931614e8ba37316acaa58639a1'],
+        'checksums': ['26df86ee233bf020b549177e1e2aaa7ad7d99cf0927d79ab3fa31c1670d09ba6'],
     }),
 ]
 
@@ -110,7 +55,6 @@ sanity_check_paths = {
 
 sanity_check_commands = [
     "bonito --help",
-    "bonito convert --help",
     "bonito download --help",
 ]
Diff against Bonito-0.3.5-fosscuda-2019b-Python-3.7.4.eb

easybuild/easyconfigs/b/Bonito/Bonito-0.3.5-fosscuda-2019b-Python-3.7.4.eb

diff --git a/easybuild/easyconfigs/b/Bonito/Bonito-0.3.5-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/b/Bonito/Bonito-0.8.1-foss-2023a-CUDA-12.1.1.eb
index 719edc53b7..83cbc16113 100644
--- a/easybuild/easyconfigs/b/Bonito/Bonito-0.3.5-fosscuda-2019b-Python-3.7.4.eb
+++ b/easybuild/easyconfigs/b/Bonito/Bonito-0.8.1-foss-2023a-CUDA-12.1.1.eb
@@ -1,103 +1,48 @@
 easyblock = 'PythonBundle'
 
 name = 'Bonito'
-version = '0.3.5'
-versionsuffix = '-Python-%(pyver)s'
+version = '0.8.1'
+versionsuffix = '-CUDA-%(cudaver)s'
 
 homepage = 'https://github.com/nanoporetech/bonito'
 description = "Convolution Basecaller for Oxford Nanopore Reads"
 
-toolchain = {'name': 'fosscuda', 'version': '2019b'}
+toolchain = {'name': 'foss', 'version': '2023a'}
 
 dependencies = [
-    ('Python', '3.7.4'),
-    ('PyTorch', '1.3.1', versionsuffix),
-    ('h5py', '2.10.0', versionsuffix),
-    ('Mako', '1.1.0'),
-    ('PyYAML', '5.1.2'),
-    ('python-parasail', '1.2', versionsuffix),
-    ('tqdm', '4.41.1'),
-    ('apex', '20200325', versionsuffix),
-    ('minimap2', '2.17'),
-    ('CuPy', '8.2.0', versionsuffix),
+    ('CUDA', '12.1.1', '', SYSTEM),
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('SciPy-bundle', '2023.07'),
+    ('PyTorch', '2.1.2', versionsuffix),
+    ('edlib', '1.3.9'),
+    ('ont-fast5-api', '4.1.2'),
+    ('ont-remora', '3.3.0', versionsuffix),
+    ('python-parasail', '1.3.4'),
+    ('pod5-file-format', '0.3.10'),
+    ('Pysam', '0.22.0'),
+    ('tqdm', '4.66.1'),
 ]
 
 use_pip = True
 
 exts_list = [
-    ('toml', '0.10.2', {
-        'checksums': ['b3bda1d108d5dd99f4a20d24d9c348e91c4db7ab1b749200bded2f839ccbe68f'],
-    }),
-    ('python-editor', '1.0.4', {
-        'modulename': 'editor',
-        'checksums': ['51fda6bcc5ddbbb7063b2af7509e43bd84bfc32a4ff71349ec7847713882327b'],
-    }),
-    ('alembic', '1.5.3', {
-        'checksums': ['04608b6904a6e6bd1af83e1a48f73f50ba214aeddef44b92d498df33818654a8'],
-    }),
-    ('cmd2', '1.5.0', {
-        'checksums': ['701a8c9975c4abc45e5d13906ab149f959f812869106347323a3f89ac0e82a62'],
-    }),
-    ('prettytable', '0.7.2', {
-        'checksums': ['2d5460dc9db74a32bcc8f9f67de68b2c4f4d2f01fa3bd518764c69156d9cacd9'],
-    }),
-    ('cliff', '3.6.0', {
-        'preinstallopts': "sed -i'' 's/cmd2.*/cmd2/g' requirements.txt && ",
-        'checksums': ['a3f4fa67eeafbcfa7cf9fe4b1755d410876528e1d0d115740db00b50a1250272'],
-    }),
-    ('colorlog', '4.7.2', {
-        'checksums': ['18d05b616438a75762d7d214b9ec3b05d274466c9f3ddd92807e755840c88251'],
-    }),
-    ('SQLAlchemy', '1.3.23', {
-        'checksums': ['6fca33672578666f657c131552c4ef8979c1606e494f78cd5199742dfb26918b'],
-    }),
-    ('cmaes', '0.7.1', {
-        'checksums': ['6476e07392b13b4de581b38fb98322b4fc9affdb5457c5f0f046a7b0bde18767'],
-    }),
-    ('optuna', '1.5.0', {
-        'checksums': ['a8847e0d13364a7e95a7dee31035a1811a2b1395feb2cf98cce7e62affb529df'],
-    }),
-    ('colorama', '0.4.4', {
-        'checksums': ['5941b2b48a20143d2267e95b1c2a7603ce057ee39fd88e7329b0c292aa16869b'],
-    }),
-    ('pyperclip', '1.8.1', {
-        'checksums': ['9abef1e79ce635eb62309ecae02dfb5a3eb952fa7d6dce09c1aef063f81424d3'],
-    }),
-    ('importlib_metadata', '2.1.1', {
-        'checksums': ['b8de9eff2b35fb037368f28a7df1df4e6436f578fa74423505b6c6a778d5b5dd'],
-    }),
-    ('stevedore', '3.3.0', {
-        'checksums': ['3a5bbd0652bf552748871eaa73a4a8dc2899786bc497a2aa1fcb4dcdb0debeee'],
-    }),
-    ('progressbar33', '2.4', {
-        'modulename': 'progressbar',
-        'checksums': ['51fe0d9b3b4023db2f983eeccdfc8c9846b84db8443b9bee002c7f58f4376eff'],
-    }),
-    ('ont-fast5-api', '3.2.0', {
-        'checksums': ['24c05250a4ee5262a3a986196ac83b51bc30e1215d90c6f0a595acb5599962e1'],
-    }),
-    ('fast-ctc-decode', '0.2.5', {
-        'source_tmpl': 'fast_ctc_decode-%(version)s-cp37-cp37m-manylinux1_x86_64.whl',
+    ('fast-ctc-decode', '0.3.6', {
+        'source_tmpl': 'fast_ctc_decode-0.3.6-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl',
         'unpack_sources': False,
-        'checksums': ['b47976b2f951dade427a2f9ddc0ae6905561a76411941cf02b7f6e3e037f4062'],
+        'checksums': ['f49994a475866edf0e61f0d9e1b41185c035ba559b8c2aa68f83342d2c80ee6b'],
     }),
-    ('mappy', '2.17', {
-        'checksums': ['ed1460efc9c6785df28065b7e93e93c92227f623a181f1a852dca6e6acb1a15f'],
+    ('mappy', '2.28', {
+        'checksums': ['0ebf7a5d62bd668f5456028215e26176e180ca68161ac18d4f7b48045484cebb'],
     }),
-    ('seqdist', '0.0.3', {
-        'preinstallopts': "sed -i 's/cupy-cuda102//g' settings.ini && ",
-        'checksums': ['bdbbea6ebba1c6dd6698d46e23ba7858f93a7cdf0c7cbc2ea66660291acb044f'],
-    }),
-    ('crf-beam', '0.0.1a0', {
-        'modulename': 'kbeam',
-        'sources': ['crf_beam-%(version)s-cp37-cp37m-manylinux1_x86_64.whl'],
-        'unpack_sources': False,
-        'checksums': ['81036ec7efd28b5d7bc758ece04c7a7c582164618744dfb64eae29352ba3e8c8'],
+    ('ont_koi', '0.4.4', {
+        'source_tmpl': 'ont_koi-0.4.4-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl',
+        'modulename': 'koi',
+        'checksums': ['e5d7c93b26363a3d4e3778f972d1f149447adbde91925e8876a97e7a63774e28'],
     }),
     ('ont-bonito', version, {
         'modulename': 'bonito',
-        'preinstallopts': "sed -i 's/==/>=/g' requirements.txt && export PATH=%(installdir)s/bin:$PATH && ",
-        'checksums': ['e280df29a5de76494a29c98f3c4946d7108f3014bfaeda214eb54a937c380335'],
+        'checksums': ['26df86ee233bf020b549177e1e2aaa7ad7d99cf0927d79ab3fa31c1670d09ba6'],
     }),
 ]
 
@@ -110,7 +55,6 @@ sanity_check_paths = {
 
 sanity_check_commands = [
     "bonito --help",
-    "bonito convert --help",
     "bonito download --help",
 ]

Updated software ont-remora-3.3.0-foss-2023a-CUDA-12.1.1.eb

Diff against ont-remora-3.3.0-foss-2023a.eb

easybuild/easyconfigs/o/ont-remora/ont-remora-3.3.0-foss-2023a.eb

diff --git a/easybuild/easyconfigs/o/ont-remora/ont-remora-3.3.0-foss-2023a.eb b/easybuild/easyconfigs/o/ont-remora/ont-remora-3.3.0-foss-2023a-CUDA-12.1.1.eb
index 7d065263f5..3fcee4f2eb 100644
--- a/easybuild/easyconfigs/o/ont-remora/ont-remora-3.3.0-foss-2023a.eb
+++ b/easybuild/easyconfigs/o/ont-remora/ont-remora-3.3.0-foss-2023a-CUDA-12.1.1.eb
@@ -2,6 +2,7 @@ easyblock = 'PythonBundle'
 
 name = 'ont-remora'
 version = '3.3.0'
+versionsuffix = '-CUDA-%(cudaver)s'
 
 homepage = 'https://github.com/nanoporetech/remora'
 description = """Methylation/modified base calling separated from basecalling. Remora primarily
@@ -12,10 +13,11 @@ and run simple inference."""
 toolchain = {'name': 'foss', 'version': '2023a'}
 
 dependencies = [
+    ('CUDA', '12.1.1', '', SYSTEM),
     ('Python', '3.11.3'),
     ('SciPy-bundle', '2023.07'),
-    ('ONNX-Runtime', '1.19.2'),
-    ('PyTorch', '2.1.2'),
+    ('ONNX-Runtime', '1.19.2', versionsuffix),
+    ('PyTorch', '2.1.2', versionsuffix),
     ('scikit-learn', '1.3.1'),
     ('tqdm', '4.66.1'),
     ('python-parasail', '1.3.4'),
@@ -29,15 +31,15 @@ use_pip = True
 
 exts_list = [
     ('thop', '0.1.1.post2209072238', {
-        'source_tmpl': SOURCE_PY3_WHL,
+        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
         'checksums': ['01473c225231927d2ad718351f78ebf7cffe6af3bed464c4f1ba1ef0f7cdda27'],
     }),
     ('mizani', '0.9.3', {
-        'source_tmpl': SOURCE_PY3_WHL,
+        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
         'checksums': ['ac5d49b913de88dc2fb28d82141e9777b97407a6971a158f758093ad5bb820a1'],
     }),
     ('plotnine', '0.12.4', {
-        'source_tmpl': SOURCE_PY3_WHL,
+        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
         'checksums': ['12748f346f107c33f3e0658ac46fbb052205ae7e97ffaf52be68310e5d29f799'],
     }),
     (name, version, {
Diff against ont-remora-1.0.0-foss-2021a.eb

easybuild/easyconfigs/o/ont-remora/ont-remora-1.0.0-foss-2021a.eb

diff --git a/easybuild/easyconfigs/o/ont-remora/ont-remora-1.0.0-foss-2021a.eb b/easybuild/easyconfigs/o/ont-remora/ont-remora-3.3.0-foss-2023a-CUDA-12.1.1.eb
index e135393f1f..3fcee4f2eb 100644
--- a/easybuild/easyconfigs/o/ont-remora/ont-remora-1.0.0-foss-2021a.eb
+++ b/easybuild/easyconfigs/o/ont-remora/ont-remora-3.3.0-foss-2023a-CUDA-12.1.1.eb
@@ -1,7 +1,8 @@
 easyblock = 'PythonBundle'
 
 name = 'ont-remora'
-version = '1.0.0'
+version = '3.3.0'
+versionsuffix = '-CUDA-%(cudaver)s'
 
 homepage = 'https://github.com/nanoporetech/remora'
 description = """Methylation/modified base calling separated from basecalling. Remora primarily
@@ -9,27 +10,41 @@ provides an API to call modified bases for basecaller programs such as Bonito.
 Remora also provides the tools to prepare datasets, train modified base models
 and run simple inference."""
 
-toolchain = {'name': 'foss', 'version': '2021a'}
+toolchain = {'name': 'foss', 'version': '2023a'}
 
 dependencies = [
-    ('Python', '3.9.5'),
-    ('SciPy-bundle', '2021.05'),
-    ('ONNX-Runtime', '1.10.0'),
-    ('PyTorch', '1.10.0'),
-    ('scikit-learn', '0.24.2'),
-    ('tqdm', '4.61.2'),
+    ('CUDA', '12.1.1', '', SYSTEM),
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('ONNX-Runtime', '1.19.2', versionsuffix),
+    ('PyTorch', '2.1.2', versionsuffix),
+    ('scikit-learn', '1.3.1'),
+    ('tqdm', '4.66.1'),
+    ('python-parasail', '1.3.4'),
+    ('polars', '0.20.2'),
+    ('Pysam', '0.22.0'),
+    ('pod5-file-format', '0.3.10'),
+    ('statsmodels', '0.14.1'),
 ]
 
 use_pip = True
 
 exts_list = [
-    ('thop', '0.0.31-2005241907', {
-        'source_tmpl': 'thop-0.0.31.post2005241907-py3-none-any.whl',
-        'checksums': ['86d67af12311b34905949eb91c8c38f92a707de72140c29a94110cc623e21ceb'],
+    ('thop', '0.1.1.post2209072238', {
+        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+        'checksums': ['01473c225231927d2ad718351f78ebf7cffe6af3bed464c4f1ba1ef0f7cdda27'],
+    }),
+    ('mizani', '0.9.3', {
+        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+        'checksums': ['ac5d49b913de88dc2fb28d82141e9777b97407a6971a158f758093ad5bb820a1'],
+    }),
+    ('plotnine', '0.12.4', {
+        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+        'checksums': ['12748f346f107c33f3e0658ac46fbb052205ae7e97ffaf52be68310e5d29f799'],
     }),
     (name, version, {
         'modulename': 'remora',
-        'checksums': ['594c7f1d4cc757c0b1d42b1af5203903df10ea11cfc6af3288d60c3df8e37d4a'],
+        'checksums': ['3c899e7333ae33ebec31c8a59650ab4d553e8a62c0abf7b03899e2ee9a0bc88a'],
     }),
 ]
Diff against ont-remora-1.0.0-foss-2021a-CUDA-11.3.1.eb

easybuild/easyconfigs/o/ont-remora/ont-remora-1.0.0-foss-2021a-CUDA-11.3.1.eb

diff --git a/easybuild/easyconfigs/o/ont-remora/ont-remora-1.0.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/o/ont-remora/ont-remora-3.3.0-foss-2023a-CUDA-12.1.1.eb
index 3298c09091..3fcee4f2eb 100644
--- a/easybuild/easyconfigs/o/ont-remora/ont-remora-1.0.0-foss-2021a-CUDA-11.3.1.eb
+++ b/easybuild/easyconfigs/o/ont-remora/ont-remora-3.3.0-foss-2023a-CUDA-12.1.1.eb
@@ -1,7 +1,7 @@
 easyblock = 'PythonBundle'
 
 name = 'ont-remora'
-version = '1.0.0'
+version = '3.3.0'
 versionsuffix = '-CUDA-%(cudaver)s'
 
 homepage = 'https://github.com/nanoporetech/remora'
@@ -10,28 +10,41 @@ provides an API to call modified bases for basecaller programs such as Bonito.
 Remora also provides the tools to prepare datasets, train modified base models
 and run simple inference."""
 
-toolchain = {'name': 'foss', 'version': '2021a'}
+toolchain = {'name': 'foss', 'version': '2023a'}
 
 dependencies = [
-    ('CUDA', '11.3.1', '', SYSTEM),
-    ('Python', '3.9.5'),
-    ('SciPy-bundle', '2021.05'),
-    ('ONNX-Runtime', '1.10.0', versionsuffix),
-    ('PyTorch', '1.10.0', versionsuffix),
-    ('scikit-learn', '0.24.2'),
-    ('tqdm', '4.61.2'),
+    ('CUDA', '12.1.1', '', SYSTEM),
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('ONNX-Runtime', '1.19.2', versionsuffix),
+    ('PyTorch', '2.1.2', versionsuffix),
+    ('scikit-learn', '1.3.1'),
+    ('tqdm', '4.66.1'),
+    ('python-parasail', '1.3.4'),
+    ('polars', '0.20.2'),
+    ('Pysam', '0.22.0'),
+    ('pod5-file-format', '0.3.10'),
+    ('statsmodels', '0.14.1'),
 ]
 
 use_pip = True
 
 exts_list = [
-    ('thop', '0.0.31-2005241907', {
-        'source_tmpl': 'thop-0.0.31.post2005241907-py3-none-any.whl',
-        'checksums': ['86d67af12311b34905949eb91c8c38f92a707de72140c29a94110cc623e21ceb'],
+    ('thop', '0.1.1.post2209072238', {
+        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+        'checksums': ['01473c225231927d2ad718351f78ebf7cffe6af3bed464c4f1ba1ef0f7cdda27'],
+    }),
+    ('mizani', '0.9.3', {
+        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+        'checksums': ['ac5d49b913de88dc2fb28d82141e9777b97407a6971a158f758093ad5bb820a1'],
+    }),
+    ('plotnine', '0.12.4', {
+        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+        'checksums': ['12748f346f107c33f3e0658ac46fbb052205ae7e97ffaf52be68310e5d29f799'],
     }),
     (name, version, {
         'modulename': 'remora',
-        'checksums': ['594c7f1d4cc757c0b1d42b1af5203903df10ea11cfc6af3288d60c3df8e37d4a'],
+        'checksums': ['3c899e7333ae33ebec31c8a59650ab4d553e8a62c0abf7b03899e2ee9a0bc88a'],
     }),
 ]

@pavelToman pavelToman mentioned this pull request Dec 5, 2024
Open
@pavelToman
Copy link
Collaborator Author

@boegelbot please test @ generoso

@boegelbot
Copy link
Collaborator

@pavelToman: Request for testing this PR well received on login1

PR test command 'EB_PR=21979 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_21979 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 14819

Test results coming soon (I hope)...

- notification for comment with ID 2520971358 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

@boegelbot
Copy link
Collaborator

Test report by @boegelbot
SUCCESS
Build succeeded for 3 out of 3 (2 easyconfigs in total)
cns1 - Linux Rocky Linux 8.9, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/boegelbot/a1bdc54a7d07eb28b54f8198d0fbebb7 for a full test report.

@pavelToman
Copy link
Collaborator Author

@boegelbot please test @ jsc-zen3

@boegelbot
Copy link
Collaborator

@pavelToman: Request for testing this PR well received on jsczen3l1.int.jsc-zen3.fz-juelich.de

PR test command 'if [[ develop != 'develop' ]]; then EB_BRANCH=develop ./easybuild_develop.sh 2> /dev/null 1>&2; EB_PREFIX=/home/boegelbot/easybuild/develop source init_env_easybuild_develop.sh; fi; EB_PR=21979 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_21979 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 5396

Test results coming soon (I hope)...

- notification for comment with ID 2521053363 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

@boegelbot
Copy link
Collaborator

Test report by @boegelbot
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.5, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.19
See https://gist.github.com/boegelbot/10ab828a6ecd30e02f8280639882349c for a full test report.

@pavelToman
Copy link
Collaborator Author

@boegelbot please test @ jsc-zen3-a100

@boegelbot
Copy link
Collaborator

@pavelToman: Request for testing this PR well received on jsczen3l1.int.jsc-zen3.fz-juelich.de

PR test command 'if [[ develop != 'develop' ]]; then EB_BRANCH=develop ./easybuild_develop.sh 2> /dev/null 1>&2; EB_PREFIX=/home/boegelbot/easybuild/develop source init_env_easybuild_develop.sh; fi; EB_PR=21979 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_21979 --ntasks=8 --partition=jsczen3g --gres=gpu:1 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 5397

Test results coming soon (I hope)...

- notification for comment with ID 2521233724 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

@boegelbot
Copy link
Collaborator

Test report by @boegelbot
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
jsczen3g1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.5, x86_64, AMD EPYC-Milan Processor (zen3), 1 x NVIDIA NVIDIA A100 80GB PCIe, 555.42.06, Python 3.9.19
See https://gist.github.com/boegelbot/0ac09c3978696868c03dd012f4ff0c82 for a full test report.

@laraPPr
Copy link
Contributor

laraPPr commented Dec 20, 2024

Test report by @laraPPr
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
node4007.donphan.os - Linux RHEL 8.8, x86_64, Intel(R) Xeon(R) Gold 6240 CPU @ 2.60GHz, 1 x NVIDIA NVIDIA A2, 545.23.08, Python 3.11.3
See https://gist.github.com/laraPPr/c978aa4bc48437b437a263fc42741426 for a full test report.

laraPPr
laraPPr approved these changes Dec 20, 2024
View reviewed changes
Copy link
Contributor

@laraPPr laraPPr left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

lgtm

@laraPPr laraPPr added this to the 4.x milestone Dec 20, 2024
@laraPPr
Copy link
Contributor

laraPPr commented Dec 20, 2024

Going in, thanks @pavelToman!

@laraPPr laraPPr merged commit 59224a8 into easybuilders:develop Dec 20, 2024
10 checks passed
@laraPPr laraPPr modified the milestones: 4.x, release after 4.9.4 Dec 20, 2024
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@laraPPr laraPPr laraPPr approved these changes

Assignees
No one assigned
Labels
update
Projects
None yet
Milestone
release after 4.9.4
Development

Successfully merging this pull request may close these issues.

Bonito
3 participants
@pavelToman @boegelbot @laraPPr