{bio}[GCCcore/14.2.0,foss/2025a] CNVkit v0.9.13, pyfaidx v0.9.0.3 w/ R 4.5.1 by JarneRenders · Pull Request #25586 · easybuilders/easybuild-easyconfigs

JarneRenders · 2026-03-19T09:03:59Z

(created using eb --new-pr)

Depends on:

{ai}[foss/2025a] PyTorch v2.9.1, Triton v3.5.1 w/ CUDA 12.8.0 from wheels #25267

…0.3-GCCcore-14.2.0.eb

github-actions · 2026-03-19T09:04:30Z

Updated software `CNVkit-0.9.13-foss-2025a-R-4.5.1.eb`

Diff against CNVkit-0.9.12-foss-2024a-R-4.4.2.eb

easybuild/easyconfigs/c/CNVkit/CNVkit-0.9.12-foss-2024a-R-4.4.2.eb

diff --git a/easybuild/easyconfigs/c/CNVkit/CNVkit-0.9.12-foss-2024a-R-4.4.2.eb b/easybuild/easyconfigs/c/CNVkit/CNVkit-0.9.13-foss-2025a-R-4.5.1.eb
index fcccfcd153..5cc16a12b9 100644
--- a/easybuild/easyconfigs/c/CNVkit/CNVkit-0.9.12-foss-2024a-R-4.4.2.eb
+++ b/easybuild/easyconfigs/c/CNVkit/CNVkit-0.9.13-foss-2025a-R-4.5.1.eb
@@ -1,46 +1,51 @@
 easyblock = 'PythonBundle'
 
 name = 'CNVkit'
-version = '0.9.12'
+version = '0.9.13'
 versionsuffix = '-R-%(rver)s'
 
 homepage = 'https://github.com/etal/cnvkit'
 description = """A command-line toolkit and Python library for detecting copy
  number variants and alterations genome-wide from high-throughput sequencing."""
 
-toolchain = {'name': 'foss', 'version': '2024a'}
+toolchain = {'name': 'foss', 'version': '2025a'}
 
-builddependencies = [('Cython', '3.0.10')]
+builddependencies = [('Cython', '3.1.1')]
 dependencies = [
-    ('Python', '3.12.3'),
-    ('SciPy-bundle', '2024.05'),
-    ('scikit-learn', '1.5.2'),
-    ('Biopython', '1.84'),
-    ('matplotlib', '3.9.2'),
-    ('networkx', '3.4.2'),
-    ('Pysam', '0.22.1'),
-    ('PyYAML', '6.0.2'),
-    ('pyfaidx', '0.8.1.2'),
-    ('R', '4.4.2'),
-    ('R-bundle-Bioconductor', '3.20', versionsuffix),
+    ('Python', '3.13.1'),
+    ('SciPy-bundle', '2025.06'),
+    ('scikit-learn', '1.7.0'),
+    ('Biopython', '1.85'),
+    ('matplotlib', '3.10.3'),
+    ('Pysam', '0.23.3'),
+    ('pyfaidx', '0.9.0.3'),
+    ('R', '4.5.1'),
+    ('R-bundle-Bioconductor', '3.22', versionsuffix),
+    ('PyTorch', '2.9.1', '-whl'),  # For pomegranate
+    ('numba', '0.62.0'),  # For apricot-select
+    ('tqdm', '4.67.1'),  # For apricot-select
 ]
 
 exts_list = [
-    ('reportlab', '4.4.9', {
-        'checksums': ['7cf487764294ee791a4781f5a157bebce262a666ae4bbb87786760a9676c9378'],
+    ('reportlab', '4.4.10', {
+        'checksums': ['5cbbb34ac3546039d0086deb2938cdec06b12da3cdb836e813258eb33cd28487'],
     }),
-    ('pomegranate', '0.15.0', {
-        # remove cython from install_requires
-        'preinstallopts': "sed -i '92d' setup.py && ",
-        'checksums': ['315207bc79375c2b98b782199a92dfcfca45234b750f8c9ccf8e3f03d37a2c10'],
+    ('apricot-select', '0.6.1', {  # Needed by pomegranate
+        'modulename': 'apricot',
+        # Only needed for tests. Nose is not compatible with newer Python
+        'preinstallopts': 'sed -i "/nose/d" setup.py && ',
+        'checksums': ['3bf872d43ee96af141c9e4c40e4359aa6ca5e3022ae43b2a8aa46b24947b8bd8'],
+    }),
+    ('pomegranate', '1.1.2', {  # Dependency will be removed in next version
+        'checksums': ['bffe01521e8783ef84cb60862ea60161c2130835868d8a37b7d79477b328ad8f'],
     }),
     (name, version, {
         'modulename': 'cnvlib',
-        'testinstall': True,
-        'runtest': 'pytest -v test',
         'source_tmpl': 'v%(version)s.tar.gz',
         'source_urls': ['https://github.com/etal/cnvkit/archive/'],
-        'checksums': ['39d65ba3d9c541dfd80986ace298b2d521067d1b81edef7169196b8dcc5d63d5'],
+        'testinstall': True,
+        'runtest': "pytest -v test",
+        'checksums': ['a197acbfb4352fdb5f661adadc5c07f19eb4ede4c15fa50dde57aa52a8d91d67'],
     }),
 ]
 
@@ -51,7 +56,7 @@ sanity_check_paths = {
 
 sanity_check_commands = [
     'cnvkit.py --help',
-    "python -s -c 'from pomegranate import base; from pomegranate.distributions import NormalDistribution'",
+    "python -s -c 'from pomegranate.hmm import DenseHMM; from pomegranate.distributions import Normal'",
 ]
 
 moduleclass = 'bio'

Diff against CNVkit-0.9.10-foss-2022b-R-4.2.2.eb

easybuild/easyconfigs/c/CNVkit/CNVkit-0.9.10-foss-2022b-R-4.2.2.eb

diff --git a/easybuild/easyconfigs/c/CNVkit/CNVkit-0.9.10-foss-2022b-R-4.2.2.eb b/easybuild/easyconfigs/c/CNVkit/CNVkit-0.9.13-foss-2025a-R-4.5.1.eb
index ad7da968cd..5cc16a12b9 100644
--- a/easybuild/easyconfigs/c/CNVkit/CNVkit-0.9.10-foss-2022b-R-4.2.2.eb
+++ b/easybuild/easyconfigs/c/CNVkit/CNVkit-0.9.13-foss-2025a-R-4.5.1.eb
@@ -1,44 +1,51 @@
 easyblock = 'PythonBundle'
 
 name = 'CNVkit'
-version = '0.9.10'
+version = '0.9.13'
 versionsuffix = '-R-%(rver)s'
 
 homepage = 'https://github.com/etal/cnvkit'
 description = """A command-line toolkit and Python library for detecting copy
  number variants and alterations genome-wide from high-throughput sequencing."""
 
-toolchain = {'name': 'foss', 'version': '2022b'}
+toolchain = {'name': 'foss', 'version': '2025a'}
 
+builddependencies = [('Cython', '3.1.1')]
 dependencies = [
-    ('Python', '3.10.8'),
-    ('scikit-learn', '1.2.1'),
-    ('Biopython', '1.81'),
-    ('matplotlib', '3.7.0'),
-    ('networkx', '3.0'),
-    ('Pillow', '9.4.0'),
-    ('Pysam', '0.21.0'),
-    ('PyYAML', '6.0'),
-    ('pyfaidx', '0.7.2.1'),
-    ('R', '4.2.2'),
-    ('R-bundle-Bioconductor', '3.16', versionsuffix),
+    ('Python', '3.13.1'),
+    ('SciPy-bundle', '2025.06'),
+    ('scikit-learn', '1.7.0'),
+    ('Biopython', '1.85'),
+    ('matplotlib', '3.10.3'),
+    ('Pysam', '0.23.3'),
+    ('pyfaidx', '0.9.0.3'),
+    ('R', '4.5.1'),
+    ('R-bundle-Bioconductor', '3.22', versionsuffix),
+    ('PyTorch', '2.9.1', '-whl'),  # For pomegranate
+    ('numba', '0.62.0'),  # For apricot-select
+    ('tqdm', '4.67.1'),  # For apricot-select
 ]
 
 exts_list = [
-    ('reportlab', '3.6.8', {
-        'checksums': ['dc7657fcb0bc3e485c3c869a44dddb52d711356a01a456664b7bef827222c982'],
+    ('reportlab', '4.4.10', {
+        'checksums': ['5cbbb34ac3546039d0086deb2938cdec06b12da3cdb836e813258eb33cd28487'],
     }),
-    ('pomegranate', '0.14.8', {
-        'checksums': ['2296651290482dd53204ffaaaea267ceee057ce1b3ef1f9d9793febe66d6693d'],
+    ('apricot-select', '0.6.1', {  # Needed by pomegranate
+        'modulename': 'apricot',
+        # Only needed for tests. Nose is not compatible with newer Python
+        'preinstallopts': 'sed -i "/nose/d" setup.py && ',
+        'checksums': ['3bf872d43ee96af141c9e4c40e4359aa6ca5e3022ae43b2a8aa46b24947b8bd8'],
+    }),
+    ('pomegranate', '1.1.2', {  # Dependency will be removed in next version
+        'checksums': ['bffe01521e8783ef84cb60862ea60161c2130835868d8a37b7d79477b328ad8f'],
     }),
     (name, version, {
         'modulename': 'cnvlib',
-        # workflow test disabled for now during build - directory available for later running
-        # 'postinstallcmds': ['cd test/ && make'],
-        'postinstallcmds': ['cp -a test %(installdir)s'],
         'source_tmpl': 'v%(version)s.tar.gz',
         'source_urls': ['https://github.com/etal/cnvkit/archive/'],
-        'checksums': ['56739496f1f59511661107e662d81e5fd8af413571e853b0a1b34d882a19349a'],
+        'testinstall': True,
+        'runtest': "pytest -v test",
+        'checksums': ['a197acbfb4352fdb5f661adadc5c07f19eb4ede4c15fa50dde57aa52a8d91d67'],
     }),
 ]
 
@@ -49,6 +56,7 @@ sanity_check_paths = {
 
 sanity_check_commands = [
     'cnvkit.py --help',
+    "python -s -c 'from pomegranate.hmm import DenseHMM; from pomegranate.distributions import Normal'",
 ]
 
 moduleclass = 'bio'

Updated software `pyfaidx-0.9.0.3-GCCcore-14.2.0.eb`

Diff against pyfaidx-0.9.0.3-GCCcore-14.3.0.eb

easybuild/easyconfigs/p/pyfaidx/pyfaidx-0.9.0.3-GCCcore-14.3.0.eb

diff --git a/easybuild/easyconfigs/p/pyfaidx/pyfaidx-0.9.0.3-GCCcore-14.3.0.eb b/easybuild/easyconfigs/p/pyfaidx/pyfaidx-0.9.0.3-GCCcore-14.2.0.eb
index 2eefed4aec..cbabff25bf 100644
--- a/easybuild/easyconfigs/p/pyfaidx/pyfaidx-0.9.0.3-GCCcore-14.3.0.eb
+++ b/easybuild/easyconfigs/p/pyfaidx/pyfaidx-0.9.0.3-GCCcore-14.2.0.eb
@@ -6,16 +6,16 @@ version = '0.9.0.3'
 homepage = 'https://pypi.python.org/pypi/pyfaidx'
 description = "pyfaidx: efficient pythonic random access to fasta subsequences"
 
-toolchain = {'name': 'GCCcore', 'version': '14.3.0'}
+toolchain = {'name': 'GCCcore', 'version': '14.2.0'}
 
 sources = [SOURCE_TAR_GZ]
 checksums = ['648b4b28d98dcb06f9a62d88a956ebb998297f4bd2f04e05609d935a2c314a79']
 
-builddependencies = [('binutils', '2.44')]
+builddependencies = [('binutils', '2.42')]
 
 dependencies = [
-    ('Python', '3.13.5'),
-    ('Python-bundle-PyPI', '2025.07'),
+    ('Python', '3.13.1'),
+    ('Python-bundle-PyPI', '2025.04'),
 ]
 
 sanity_check_paths = {

Diff against pyfaidx-0.7.1-GCCcore-12.3.0-Python-2.7.18.eb

easybuild/easyconfigs/p/pyfaidx/pyfaidx-0.7.1-GCCcore-12.3.0-Python-2.7.18.eb

diff --git a/easybuild/easyconfigs/p/pyfaidx/pyfaidx-0.7.1-GCCcore-12.3.0-Python-2.7.18.eb b/easybuild/easyconfigs/p/pyfaidx/pyfaidx-0.9.0.3-GCCcore-14.2.0.eb
index 2eee8fea50..cbabff25bf 100644
--- a/easybuild/easyconfigs/p/pyfaidx/pyfaidx-0.7.1-GCCcore-12.3.0-Python-2.7.18.eb
+++ b/easybuild/easyconfigs/p/pyfaidx/pyfaidx-0.9.0.3-GCCcore-14.2.0.eb
@@ -1,27 +1,21 @@
-easyblock = 'PythonBundle'
+easyblock = 'PythonPackage'
 
 name = 'pyfaidx'
-version = '0.7.1'
-versionsuffix = '-Python-%(pyver)s'
+version = '0.9.0.3'
 
 homepage = 'https://pypi.python.org/pypi/pyfaidx'
 description = "pyfaidx: efficient pythonic random access to fasta subsequences"
 
-toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchain = {'name': 'GCCcore', 'version': '14.2.0'}
 
-builddependencies = [
-    ('binutils', '2.40'),
-]
+sources = [SOURCE_TAR_GZ]
+checksums = ['648b4b28d98dcb06f9a62d88a956ebb998297f4bd2f04e05609d935a2c314a79']
 
-dependencies = [('Python', '2.7.18')]
+builddependencies = [('binutils', '2.42')]
 
-exts_list = [
-    ('six', '1.17.0', {
-        'checksums': ['ff70335d468e7eb6ec65b95b99d3a2836546063f63acc5171de367e834932a81'],
-    }),
-    (name, version, {
-        'checksums': ['3977632b7fd29049f8b11035d7e9dea0e2c5da9c235f982b4c3fae06ff1fa23f'],
-    }),
+dependencies = [
+    ('Python', '3.13.1'),
+    ('Python-bundle-PyPI', '2025.04'),
 ]
 
 sanity_check_paths = {

Diff against pyfaidx-0.8.1.2-GCCcore-13.3.0.eb

easybuild/easyconfigs/p/pyfaidx/pyfaidx-0.8.1.2-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/p/pyfaidx/pyfaidx-0.8.1.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/pyfaidx/pyfaidx-0.9.0.3-GCCcore-14.2.0.eb
index 62b2350481..cbabff25bf 100644
--- a/easybuild/easyconfigs/p/pyfaidx/pyfaidx-0.8.1.2-GCCcore-13.3.0.eb
+++ b/easybuild/easyconfigs/p/pyfaidx/pyfaidx-0.9.0.3-GCCcore-14.2.0.eb
@@ -1,21 +1,21 @@
 easyblock = 'PythonPackage'
 
 name = 'pyfaidx'
-version = '0.8.1.2'
+version = '0.9.0.3'
 
 homepage = 'https://pypi.python.org/pypi/pyfaidx'
 description = "pyfaidx: efficient pythonic random access to fasta subsequences"
 
-toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+toolchain = {'name': 'GCCcore', 'version': '14.2.0'}
 
 sources = [SOURCE_TAR_GZ]
-checksums = ['d8452470455b1e778f93969447db8ea24deb4624c7c40769516459cb6f87bc33']
+checksums = ['648b4b28d98dcb06f9a62d88a956ebb998297f4bd2f04e05609d935a2c314a79']
 
 builddependencies = [('binutils', '2.42')]
 
 dependencies = [
-    ('Python', '3.12.3'),
-    ('Python-bundle-PyPI', '2024.06'),
+    ('Python', '3.13.1'),
+    ('Python-bundle-PyPI', '2025.04'),
 ]
 
 sanity_check_paths = {

adding easyconfigs: CNVkit-0.9.13-foss-2025a-R-4.5.1.eb, pyfaidx-0.9.…

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…0.3-GCCcore-14.2.0.eb

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{bio}[GCCcore/14.2.0,foss/2025a] CNVkit v0.9.13, pyfaidx v0.9.0.3 w/ R 4.5.1#25586

{bio}[GCCcore/14.2.0,foss/2025a] CNVkit v0.9.13, pyfaidx v0.9.0.3 w/ R 4.5.1#25586
JarneRenders wants to merge 1 commit intoeasybuilders:developfrom
JarneRenders:20260319100355_new_pr_CNVkit0913

JarneRenders commented Mar 19, 2026 •

edited

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JarneRenders commented Mar 19, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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Updated software CNVkit-0.9.13-foss-2025a-R-4.5.1.eb

Updated software pyfaidx-0.9.0.3-GCCcore-14.2.0.eb

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JarneRenders commented Mar 19, 2026 •

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Updated software `CNVkit-0.9.13-foss-2025a-R-4.5.1.eb`

Updated software `pyfaidx-0.9.0.3-GCCcore-14.2.0.eb`