Adding easyconfig medaka-2.0.1-foss-2023a.eb #22001

MaximeVdB · 2024-12-10T14:54:54Z

Medaka v2 now relies on PyTorch instead of TensorFlow and also needs tqdm.

Building with WITHDEFLATE=1 since otherwise the medaka import sanity check fails because libmedaka.abi3.so is missing certain libdeflate-related symbols. Libdeflate is also supposed to help the BAM file IO (https://github.com/nanoporetech/medaka/releases/tag/v1.6.0).

Medaka v2 now relies on PyTorch instead of TensorFlow and also needs tqdm. Building with WITHDEFLATE=1 since otherwise the medaka import sanity check fails because libmedaka.abi3.so is missing certain libdeflate-related symbols. Libdeflate is also supposed to help the BAM file IO (https://github.com/nanoporetech/medaka/releases/tag/v1.6.0).

github-actions · 2024-12-10T14:55:28Z

Updated software `medaka-2.0.1-foss-2023a.eb`

Diff against medaka-1.12.1-foss-2023a-CUDA-12.1.1.eb

easybuild/easyconfigs/m/medaka/medaka-1.12.1-foss-2023a-CUDA-12.1.1.eb

diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.12.1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/m/medaka/medaka-2.0.1-foss-2023a.eb
index 3e055e5d8d..0222c35bc1 100644
--- a/easybuild/easyconfigs/m/medaka/medaka-1.12.1-foss-2023a-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/m/medaka/medaka-2.0.1-foss-2023a.eb
@@ -1,18 +1,7 @@
-# This is a contribution from HPCNow! (http://hpcnow.com)
-# Copyright::   HPCNow!
-# Authors::     Danilo Gonzalez <danilo.gonzalez@hpcnow.com>
-# License::     GPL-v3.0
-# Updated to foss-2020b to use with artic tool
-# J. Sassmannshausen (GSTT/NHS UK)
-# Updated to 1.5.0
-# Jasper Grimm (UoY)
-# Updated: Petr Král (INUITS)
-
 easyblock = 'PythonBundle'
 
 name = 'medaka'
-version = '1.12.1'
-versionsuffix = '-CUDA-%(cudaver)s'
+version = '2.0.1'
 
 homepage = 'https://github.com/nanoporetech/medaka'
 description = "medaka is a tool to create a consensus sequence from nanopore sequencing data."
@@ -24,10 +13,9 @@ builddependencies = [('Autotools', '20220317')]
 
 _minimap_ver = '2.26'
 dependencies = [
-    ('CUDA', '12.1.1', '', SYSTEM),
     ('Python', '3.11.3'),
     ('Python-bundle-PyPI', '2023.06'),  # includes cffi
-    ('TensorFlow', '2.15.1', versionsuffix),
+    ('PyTorch', '2.1.2'),
     ('Pysam', '0.22.0'),
     ('SAMtools', '1.18'),
     ('minimap2', _minimap_ver),
@@ -40,17 +28,17 @@ dependencies = [
     ('WhatsHap', '2.2'),
     ('intervaltree-python', '3.1.0'),
     ('BCFtools', '1.18'),
+    ('libdeflate', '1.18'),
+    ('tqdm', '4.66.1'),
 ]
 
 use_pip = True
 sanity_pip_check = True
 
 local_sed_commands = [
-    "sed -i 's/tensorflow.*/tensorflow/g;s/cffi==1.15.0/cffi/g' requirements.txt pyproject.toml",
-    # Python 3.11 support
-    "sed -i 's/8, 9, 10/8, 9, 10, 11/g;s/,<3.11//g' setup.py",
-    # ont-parasail on PyPI is just pre-built wheels for (python-)parasail
-    "sed -i 's/ont-parasail/parasail/g' requirements.txt",
+    "sed -i 's/torch.*/torch/g' requirements.txt pyproject.toml",
+    # ont-mappy/ont-parasail on PyPI are just pre-built wheels for mappy/(python-)parasail
+    "sed -i 's/ont-mappy/mappy/g;s/ont-parasail/parasail/g' requirements.txt",
 ]
 
 exts_list = [
@@ -61,17 +49,17 @@ exts_list = [
         'source_tmpl': SOURCE_PY3_WHL,
         'checksums': ['0b2749c2cde3ef640bf314a9f94b24d929fe1ca476974719a6909dfc568c3aac'],
     }),
-    # medaka 1.12.0 requires h5py ~=3.10.0
+    # medaka >= 1.12.0 requires h5py ~=3.10.0
     ('h5py', '3.10.0', {
         'checksums': ['d93adc48ceeb33347eb24a634fb787efc7ae4644e6ea4ba733d099605045c049'],
     }),
-    ('pyabpoa', '1.5.2', {
-        'checksums': ['be39c83b12e923c9e47073cb8f0abc4c42f609fa2c0ec13d6f6a4f5a0537ee06'],
+    ('pyabpoa', '1.5.3', {
+        'checksums': ['94714bb5c6be9f5ca35b66a5c63490237ebff2498ff93b82a842a9512b0bbc08'],
     }),
     (name, version, {
-        'checksums': ['df4baf7d1e9154de85229aef237919619ff6ae7f7d103abb0828e449ff977adf'],
+        'checksums': ['7b7a0dc558f19d10fe8eb588f709a179ef5204a53aad5cfdfbd5c57039193a9f'],
         # Some requirements are too strict.
-        'preinstallopts': " && ".join(local_sed_commands) + " && ",
+        'preinstallopts': " && ".join(local_sed_commands) + " && WITHDEFLATE=1 ",
     }),
 ]

Diff against medaka-1.12.1-foss-2023a.eb

easybuild/easyconfigs/m/medaka/medaka-1.12.1-foss-2023a.eb

diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.12.1-foss-2023a.eb b/easybuild/easyconfigs/m/medaka/medaka-2.0.1-foss-2023a.eb
index f95d01c89d..0222c35bc1 100644
--- a/easybuild/easyconfigs/m/medaka/medaka-1.12.1-foss-2023a.eb
+++ b/easybuild/easyconfigs/m/medaka/medaka-2.0.1-foss-2023a.eb
@@ -1,17 +1,7 @@
-# This is a contribution from HPCNow! (http://hpcnow.com)
-# Copyright::   HPCNow!
-# Authors::     Danilo Gonzalez <danilo.gonzalez@hpcnow.com>
-# License::     GPL-v3.0
-# Updated to foss-2020b to use with artic tool
-# J. Sassmannshausen (GSTT/NHS UK)
-# Updated to 1.5.0
-# Jasper Grimm (UoY)
-# Updated: Petr Král (INUITS)
-
 easyblock = 'PythonBundle'
 
 name = 'medaka'
-version = '1.12.1'
+version = '2.0.1'
 
 homepage = 'https://github.com/nanoporetech/medaka'
 description = "medaka is a tool to create a consensus sequence from nanopore sequencing data."
@@ -25,7 +15,7 @@ _minimap_ver = '2.26'
 dependencies = [
     ('Python', '3.11.3'),
     ('Python-bundle-PyPI', '2023.06'),  # includes cffi
-    ('TensorFlow', '2.13.0'),
+    ('PyTorch', '2.1.2'),
     ('Pysam', '0.22.0'),
     ('SAMtools', '1.18'),
     ('minimap2', _minimap_ver),
@@ -38,17 +28,17 @@ dependencies = [
     ('WhatsHap', '2.2'),
     ('intervaltree-python', '3.1.0'),
     ('BCFtools', '1.18'),
+    ('libdeflate', '1.18'),
+    ('tqdm', '4.66.1'),
 ]
 
 use_pip = True
 sanity_pip_check = True
 
 local_sed_commands = [
-    "sed -i 's/tensorflow.*/tensorflow/g;s/cffi==1.15.0/cffi/g' requirements.txt pyproject.toml",
-    # Python 3.11 support
-    "sed -i 's/8, 9, 10/8, 9, 10, 11/g;s/,<3.11//g' setup.py",
-    # ont-parasail on PyPI is just pre-built wheels for (python-)parasail
-    "sed -i 's/ont-parasail/parasail/g' requirements.txt",
+    "sed -i 's/torch.*/torch/g' requirements.txt pyproject.toml",
+    # ont-mappy/ont-parasail on PyPI are just pre-built wheels for mappy/(python-)parasail
+    "sed -i 's/ont-mappy/mappy/g;s/ont-parasail/parasail/g' requirements.txt",
 ]
 
 exts_list = [
@@ -59,17 +49,17 @@ exts_list = [
         'source_tmpl': SOURCE_PY3_WHL,
         'checksums': ['0b2749c2cde3ef640bf314a9f94b24d929fe1ca476974719a6909dfc568c3aac'],
     }),
-    # medaka 1.12.0 requires h5py ~=3.10.0
+    # medaka >= 1.12.0 requires h5py ~=3.10.0
     ('h5py', '3.10.0', {
         'checksums': ['d93adc48ceeb33347eb24a634fb787efc7ae4644e6ea4ba733d099605045c049'],
     }),
-    ('pyabpoa', '1.5.2', {
-        'checksums': ['be39c83b12e923c9e47073cb8f0abc4c42f609fa2c0ec13d6f6a4f5a0537ee06'],
+    ('pyabpoa', '1.5.3', {
+        'checksums': ['94714bb5c6be9f5ca35b66a5c63490237ebff2498ff93b82a842a9512b0bbc08'],
     }),
     (name, version, {
-        'checksums': ['df4baf7d1e9154de85229aef237919619ff6ae7f7d103abb0828e449ff977adf'],
+        'checksums': ['7b7a0dc558f19d10fe8eb588f709a179ef5204a53aad5cfdfbd5c57039193a9f'],
         # Some requirements are too strict.
-        'preinstallopts': " && ".join(local_sed_commands) + " && ",
+        'preinstallopts': " && ".join(local_sed_commands) + " && WITHDEFLATE=1 ",
     }),
 ]

Diff against medaka-1.12.0-foss-2023a-CUDA-12.1.1.eb

easybuild/easyconfigs/m/medaka/medaka-1.12.0-foss-2023a-CUDA-12.1.1.eb

diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.12.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/m/medaka/medaka-2.0.1-foss-2023a.eb
index c9ac4870bf..0222c35bc1 100644
--- a/easybuild/easyconfigs/m/medaka/medaka-1.12.0-foss-2023a-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/m/medaka/medaka-2.0.1-foss-2023a.eb
@@ -1,18 +1,7 @@
-# This is a contribution from HPCNow! (http://hpcnow.com)
-# Copyright::   HPCNow!
-# Authors::     Danilo Gonzalez <danilo.gonzalez@hpcnow.com>
-# License::     GPL-v3.0
-# Updated to foss-2020b to use with artic tool
-# J. Sassmannshausen (GSTT/NHS UK)
-# Updated to 1.5.0
-# Jasper Grimm (UoY)
-# Updated: Petr Král (INUITS)
-
 easyblock = 'PythonBundle'
 
 name = 'medaka'
-version = '1.12.0'
-versionsuffix = '-CUDA-%(cudaver)s'
+version = '2.0.1'
 
 homepage = 'https://github.com/nanoporetech/medaka'
 description = "medaka is a tool to create a consensus sequence from nanopore sequencing data."
@@ -24,10 +13,9 @@ builddependencies = [('Autotools', '20220317')]
 
 _minimap_ver = '2.26'
 dependencies = [
-    ('CUDA', '12.1.1', '', SYSTEM),
     ('Python', '3.11.3'),
     ('Python-bundle-PyPI', '2023.06'),  # includes cffi
-    ('TensorFlow', '2.15.1', versionsuffix),
+    ('PyTorch', '2.1.2'),
     ('Pysam', '0.22.0'),
     ('SAMtools', '1.18'),
     ('minimap2', _minimap_ver),
@@ -40,15 +28,17 @@ dependencies = [
     ('WhatsHap', '2.2'),
     ('intervaltree-python', '3.1.0'),
     ('BCFtools', '1.18'),
+    ('libdeflate', '1.18'),
+    ('tqdm', '4.66.1'),
 ]
 
 use_pip = True
 sanity_pip_check = True
 
 local_sed_commands = [
-    "sed -i 's/tensorflow.*/tensorflow/g;s/cffi==1.15.0/cffi/g' requirements.txt pyproject.toml",
-    # Python 3.11 support
-    "sed -i 's/8, 9, 10/8, 9, 10, 11/g;s/,<3.11//g' setup.py",
+    "sed -i 's/torch.*/torch/g' requirements.txt pyproject.toml",
+    # ont-mappy/ont-parasail on PyPI are just pre-built wheels for mappy/(python-)parasail
+    "sed -i 's/ont-mappy/mappy/g;s/ont-parasail/parasail/g' requirements.txt",
 ]
 
 exts_list = [
@@ -59,16 +49,17 @@ exts_list = [
         'source_tmpl': SOURCE_PY3_WHL,
         'checksums': ['0b2749c2cde3ef640bf314a9f94b24d929fe1ca476974719a6909dfc568c3aac'],
     }),
+    # medaka >= 1.12.0 requires h5py ~=3.10.0
     ('h5py', '3.10.0', {
         'checksums': ['d93adc48ceeb33347eb24a634fb787efc7ae4644e6ea4ba733d099605045c049'],
     }),
-    ('pyabpoa', '1.5.1', {
-        'checksums': ['878f981e890a421d92a0d7606705d0ad9813ae6086239460dfe4b0cfc7476174'],
+    ('pyabpoa', '1.5.3', {
+        'checksums': ['94714bb5c6be9f5ca35b66a5c63490237ebff2498ff93b82a842a9512b0bbc08'],
     }),
     (name, version, {
-        'checksums': ['039219204111a8114b1f72d87d0d3463e43473790cff4520c8afbd79cc8784d6'],
+        'checksums': ['7b7a0dc558f19d10fe8eb588f709a179ef5204a53aad5cfdfbd5c57039193a9f'],
         # Some requirements are too strict.
-        'preinstallopts': " && ".join(local_sed_commands) + " && ",
+        'preinstallopts': " && ".join(local_sed_commands) + " && WITHDEFLATE=1 ",
     }),
 ]

PhoenixEmik · 2024-12-12T10:16:45Z

easybuild/easyconfigs/m/medaka/medaka-2.0.1-foss-2023a.eb

+dependencies = [
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),  # includes cffi
+    ('PyTorch', '2.1.2'),


PyTorch version should be 2.3 or 2.3.1 according to https://github.com/nanoporetech/medaka/blob/03b58482ca38088790edfa4b196f8bf619f83c05/requirements.txt#L18

github-actions bot added the update label Dec 10, 2024

PhoenixEmik suggested changes Feb 11, 2025

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Adding easyconfig medaka-2.0.1-foss-2023a.eb #22001

Adding easyconfig medaka-2.0.1-foss-2023a.eb #22001

MaximeVdB commented Dec 10, 2024

github-actions bot commented Dec 10, 2024

PhoenixEmik Dec 12, 2024

Adding easyconfig medaka-2.0.1-foss-2023a.eb #22001

Are you sure you want to change the base?

Adding easyconfig medaka-2.0.1-foss-2023a.eb #22001

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MaximeVdB commented Dec 10, 2024

github-actions bot commented Dec 10, 2024

Updated software medaka-2.0.1-foss-2023a.eb

PhoenixEmik Dec 12, 2024

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Updated software `medaka-2.0.1-foss-2023a.eb`