{bio}[foss/2023b] CrossMap 0.7.3

[fizwit]

(created using eb --new-pr)

[github-actions]

Updated software bx-python-0.13.0-foss-2023b.eb

Diff against bx-python-0.10.0-foss-2023a.eb

easybuild/easyconfigs/b/bx-python/bx-python-0.10.0-foss-2023a.eb

diff --git a/easybuild/easyconfigs/b/bx-python/bx-python-0.10.0-foss-2023a.eb b/easybuild/easyconfigs/b/bx-python/bx-python-0.13.0-foss-2023b.eb
index da5a1cb4e5..2b6e52f121 100644
--- a/easybuild/easyconfigs/b/bx-python/bx-python-0.10.0-foss-2023a.eb
+++ b/easybuild/easyconfigs/b/bx-python/bx-python-0.13.0-foss-2023b.eb
@@ -1,21 +1,22 @@
 easyblock = 'PythonBundle'
 
 name = 'bx-python'
-version = '0.10.0'
+version = '0.13.0'
 
 homepage = 'https://github.com/bxlab/bx-python'
 description = """The bx-python project is a Python library and associated set of scripts to allow for rapid
  implementation of genome scale analyses."""
 
-toolchain = {'name': 'foss', 'version': '2023a'}
+toolchain = {'name': 'foss', 'version': '2023b'}
 
 dependencies = [
-    ('Python', '3.11.3'),
+    ('Python', '3.11.5'),
     ('LZO', '2.10'),
-    ('SciPy-bundle', '2023.07'),
+    ('SciPy-bundle', '2023.11'),
 ]
 
 use_pip = True
+sanity_pip_check = True
 
 exts_list = [
     ('python-lzo', '1.15', {
@@ -23,12 +24,12 @@ exts_list = [
         'preinstallopts': "export PREFIX=$EBROOTLZO && ",
         'checksums': ['a57aaa00c5c3a0515dd9f7426ba2cf601767dc19dc023d8b99d4a13b0a327b49'],
     }),
-    (name, version, {
+    ('bx_python', version, {
         'modulename': 'bx',
-        'checksums': ['bfe9541d7b18a98e907b085e31f58d3989fbca4dc667c4ae48c33b753e0e2da8'],
+        'checksums': ['ce04696543367efc6b7995d9463efeda691b9a58f6f55a7bd831e642159b0644'],
     }),
 ]
 
-sanity_pip_check = True
+sanity_check_commands = ['bnMapper.py --help']
 
 moduleclass = 'bio'

Diff against bx-python-0.9.0-foss-2022a.eb

easybuild/easyconfigs/b/bx-python/bx-python-0.9.0-foss-2022a.eb

diff --git a/easybuild/easyconfigs/b/bx-python/bx-python-0.9.0-foss-2022a.eb b/easybuild/easyconfigs/b/bx-python/bx-python-0.13.0-foss-2023b.eb
index 39af310846..2b6e52f121 100644
--- a/easybuild/easyconfigs/b/bx-python/bx-python-0.9.0-foss-2022a.eb
+++ b/easybuild/easyconfigs/b/bx-python/bx-python-0.13.0-foss-2023b.eb
@@ -1,34 +1,35 @@
 easyblock = 'PythonBundle'
 
 name = 'bx-python'
-version = '0.9.0'
+version = '0.13.0'
 
 homepage = 'https://github.com/bxlab/bx-python'
 description = """The bx-python project is a Python library and associated set of scripts to allow for rapid
  implementation of genome scale analyses."""
 
-toolchain = {'name': 'foss', 'version': '2022a'}
+toolchain = {'name': 'foss', 'version': '2023b'}
 
 dependencies = [
-    ('Python', '3.10.4'),
+    ('Python', '3.11.5'),
     ('LZO', '2.10'),
-    ('SciPy-bundle', '2022.05'),
+    ('SciPy-bundle', '2023.11'),
 ]
 
 use_pip = True
+sanity_pip_check = True
 
 exts_list = [
-    ('python-lzo', '1.14', {
+    ('python-lzo', '1.15', {
         'modulename': 'lzo',
         'preinstallopts': "export PREFIX=$EBROOTLZO && ",
-        'checksums': ['83cbd8ecaae284735250e31d6c0ecc18ac08763fab2a8c910dc5a6910db6250c'],
+        'checksums': ['a57aaa00c5c3a0515dd9f7426ba2cf601767dc19dc023d8b99d4a13b0a327b49'],
     }),
-    (name, version, {
+    ('bx_python', version, {
         'modulename': 'bx',
-        'checksums': ['fe545c44d2ea74b239d41e9090618aaf6a859d1a1f64b4a21b133cb602dfdb49'],
+        'checksums': ['ce04696543367efc6b7995d9463efeda691b9a58f6f55a7bd831e642159b0644'],
     }),
 ]
 
-sanity_pip_check = True
+sanity_check_commands = ['bnMapper.py --help']
 
 moduleclass = 'bio'

Diff against bx-python-0.8.13-foss-2021b.eb

easybuild/easyconfigs/b/bx-python/bx-python-0.8.13-foss-2021b.eb

diff --git a/easybuild/easyconfigs/b/bx-python/bx-python-0.8.13-foss-2021b.eb b/easybuild/easyconfigs/b/bx-python/bx-python-0.13.0-foss-2023b.eb
index 70cc43c9f9..2b6e52f121 100644
--- a/easybuild/easyconfigs/b/bx-python/bx-python-0.8.13-foss-2021b.eb
+++ b/easybuild/easyconfigs/b/bx-python/bx-python-0.13.0-foss-2023b.eb
@@ -1,34 +1,35 @@
 easyblock = 'PythonBundle'
 
 name = 'bx-python'
-version = '0.8.13'
+version = '0.13.0'
 
 homepage = 'https://github.com/bxlab/bx-python'
 description = """The bx-python project is a Python library and associated set of scripts to allow for rapid
  implementation of genome scale analyses."""
 
-toolchain = {'name': 'foss', 'version': '2021b'}
+toolchain = {'name': 'foss', 'version': '2023b'}
 
 dependencies = [
-    ('Python', '3.9.6'),
+    ('Python', '3.11.5'),
     ('LZO', '2.10'),
-    ('SciPy-bundle', '2021.10'),
+    ('SciPy-bundle', '2023.11'),
 ]
 
 use_pip = True
+sanity_pip_check = True
 
 exts_list = [
-    ('python-lzo', '1.14', {
+    ('python-lzo', '1.15', {
         'modulename': 'lzo',
         'preinstallopts': "export PREFIX=$EBROOTLZO && ",
-        'checksums': ['83cbd8ecaae284735250e31d6c0ecc18ac08763fab2a8c910dc5a6910db6250c'],
+        'checksums': ['a57aaa00c5c3a0515dd9f7426ba2cf601767dc19dc023d8b99d4a13b0a327b49'],
     }),
-    (name, version, {
+    ('bx_python', version, {
         'modulename': 'bx',
-        'checksums': ['5989170d13367e9f811014803bafdbcc893024d63e98b66f734511e4f9e90c7d'],
+        'checksums': ['ce04696543367efc6b7995d9463efeda691b9a58f6f55a7bd831e642159b0644'],
     }),
 ]
 
-sanity_pip_check = True
+sanity_check_commands = ['bnMapper.py --help']
 
 moduleclass = 'bio'

Updated software CrossMap-0.7.3-foss-2023b.eb

Diff against CrossMap-0.3.9-foss-2019a-Python-3.7.2.eb

easybuild/easyconfigs/c/CrossMap/CrossMap-0.3.9-foss-2019a-Python-3.7.2.eb

diff --git a/easybuild/easyconfigs/c/CrossMap/CrossMap-0.3.9-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/c/CrossMap/CrossMap-0.7.3-foss-2023b.eb
index 14f5d6572e..90210916e1 100644
--- a/easybuild/easyconfigs/c/CrossMap/CrossMap-0.3.9-foss-2019a-Python-3.7.2.eb
+++ b/easybuild/easyconfigs/c/CrossMap/CrossMap-0.7.3-foss-2023b.eb
@@ -1,34 +1,39 @@
 easyblock = 'PythonPackage'
 
 name = 'CrossMap'
-version = '0.3.9'
-versionsuffix = '-Python-%(pyver)s'
+version = '0.7.3'
 
-homepage = 'http://crossmap.sourceforge.net'
+homepage = 'https://crossmap.readthedocs.io/'
 description = """CrossMap is a program for genome coordinates conversion
  between different assemblies (such as hg18 (NCBI36) <=> hg19 (GRCh37)).
  It supports commonly used file formats including BAM, CRAM, SAM, Wiggle,
  BigWig, BED, GFF, GTF and VCF."""
 
-toolchain = {'name': 'foss', 'version': '2019a'}
+toolchain = {'name': 'foss', 'version': '2023b'}
 
-sources = [SOURCE_TAR_GZ]
-checksums = ['e20a4653e9fc313ac0f5a6cfc37b42e83c3cf2b42f9483706cfb9ec9ff72c74c']
+# 0.7.3 download from PyPi reports version of 0.7.0. Download from github to
+# find latest version
+local_commit = '8a230bd19a334b545b9ef68cc594b7fb6cbc84e8'
+
+source_urls = ['https://github.com/liguowang/CrossMap/archive']
+sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}]
+checksums = ['d33b0da3cf9d44e077a23fc6ab89a41a1d8abb0fcd62e1334c86e1027c647f4c']
 
 dependencies = [
-    ('Python', '3.7.2'),
-    ('bx-python', '0.8.4'),
-    ('pyBigWig', '0.3.17'),
-    ('Pysam', '0.15.2'),
+    ('Python', '3.11.5'),
+    ('bx-python', '0.13.0'),
+    ('pyBigWig', '0.3.23'),
+    ('Pysam', '0.22.0'),
 ]
 
 use_pip = True
 download_dep_fail = True
+sanity_pip_check = True
 
-sanity_check_commands = [('CrossMap.py', '')]
+sanity_check_commands = [('CrossMap', '--help')]
 
 sanity_check_paths = {
-    'files': ['bin/CrossMap.py'],
+    'files': ['bin/CrossMap'],
     'dirs': ['lib/python%(pyshortver)s/site-packages'],
 }
 

Updated software pyBigWig-0.3.23-gfbf-2023b.eb

Diff against pyBigWig-0.3.22-gfbf-2023a.eb

easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.22-gfbf-2023a.eb

diff --git a/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.22-gfbf-2023a.eb b/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.23-gfbf-2023b.eb
index 8e9947f8e5..25ea4ec30c 100644
--- a/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.22-gfbf-2023a.eb
+++ b/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.23-gfbf-2023b.eb
@@ -1,22 +1,22 @@
 easyblock = 'PythonPackage'
 
 name = 'pyBigWig'
-version = '0.3.22'
+version = '0.3.23'
 
 homepage = 'https://github.com/deeptools/pyBigWig'
 description = """A python extension, written in C, for quick access to bigBed
 files and access to and creation of bigWig files."""
 
-toolchain = {'name': 'gfbf', 'version': '2023a'}
+toolchain = {'name': 'gfbf', 'version': '2023b'}
 
-sources = [SOURCE_TAR_GZ]
-checksums = ['5d4426f754bd7b7f6dc21d6c3f93b58a96a65b6eb2e578ae03b31a71272d2243']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['b780c2b77f024c7967d7bd2eca0fa39a4d939c86b807135960e26faafafbec84']
 
 dependencies = [
-    ('Python', '3.11.3'),
-    ('cURL', '8.0.1'),
-    ('NSS', '3.89.1'),    # provides libfreebl3
-    ('SciPy-bundle', '2023.07'),    # optional, for numpy support
+    ('Python', '3.11.5'),
+    ('cURL', '8.3.0'),
+    ('NSS', '3.94'),    # provides libfreebl3
+    ('SciPy-bundle', '2023.11'),    # optional, for numpy support
 ]
 
 use_pip = True

Diff against pyBigWig-0.3.22-foss-2022b.eb

easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.22-foss-2022b.eb

diff --git a/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.22-foss-2022b.eb b/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.23-gfbf-2023b.eb
index 723a23aefb..25ea4ec30c 100644
--- a/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.22-foss-2022b.eb
+++ b/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.23-gfbf-2023b.eb
@@ -1,31 +1,24 @@
 easyblock = 'PythonPackage'
 
 name = 'pyBigWig'
-version = '0.3.22'
+version = '0.3.23'
 
-github_account = 'deeptools'
-homepage = 'https://github.com/%(github_account)s/%(name)s'
+homepage = 'https://github.com/deeptools/pyBigWig'
 description = """A python extension, written in C, for quick access to bigBed
- files and access to and creation of bigWig files."""
+files and access to and creation of bigWig files."""
 
-toolchain = {'name': 'foss', 'version': '2022b'}
+toolchain = {'name': 'gfbf', 'version': '2023b'}
 
-source_urls = [GITHUB_SOURCE]
-sources = ['%(version)s.tar.gz']
-checksums = ['3b8d62b2bedcee0545a586884466c97a64b64283a309b211300b670f41dd2046']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['b780c2b77f024c7967d7bd2eca0fa39a4d939c86b807135960e26faafafbec84']
 
 dependencies = [
-    ('Python', '3.10.8'),
-    ('cURL', '7.86.0'),
-    ('NSS', '3.85'),    # provides libfreebl3
-    ('SciPy-bundle', '2023.02'),    # optional, for numpy support
+    ('Python', '3.11.5'),
+    ('cURL', '8.3.0'),
+    ('NSS', '3.94'),    # provides libfreebl3
+    ('SciPy-bundle', '2023.11'),    # optional, for numpy support
 ]
 
-# fix  version of '0.0.0' issue
-preinstallopts = """sed -i 's/setup(/setup(version="%(version)s",/g' setup.py && """
-# do not use setuptools-scm to detect version
-preinstallopts += """sed -i 's/[tool.setuptools_scm]//' pyproject.toml && """
-
 use_pip = True
 download_dep_fail = True
 

Diff against pyBigWig-0.3.18-foss-2022a.eb

easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.18-foss-2022a.eb

diff --git a/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.18-foss-2022a.eb b/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.23-gfbf-2023b.eb
index 52abcea467..25ea4ec30c 100644
--- a/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.18-foss-2022a.eb
+++ b/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.23-gfbf-2023b.eb
@@ -1,24 +1,22 @@
 easyblock = 'PythonPackage'
 
 name = 'pyBigWig'
-version = '0.3.18'
+version = '0.3.23'
 
-github_account = 'deeptools'
-homepage = 'https://github.com/%(github_account)s/%(name)s'
+homepage = 'https://github.com/deeptools/pyBigWig'
 description = """A python extension, written in C, for quick access to bigBed
- files and access to and creation of bigWig files."""
+files and access to and creation of bigWig files."""
 
-toolchain = {'name': 'foss', 'version': '2022a'}
+toolchain = {'name': 'gfbf', 'version': '2023b'}
 
-source_urls = [GITHUB_SOURCE]
-sources = ['%(version)s.tar.gz']
-checksums = ['552564d8ce8720a8ae70ed5e5534617fb0cab306b666468d1c61b6d389b8a10c']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['b780c2b77f024c7967d7bd2eca0fa39a4d939c86b807135960e26faafafbec84']
 
 dependencies = [
-    ('Python', '3.10.4'),
-    ('cURL', '7.83.0'),
-    ('NSS', '3.79'),    # provides libfreebl3
-    ('SciPy-bundle', '2022.05'),    # optional, for numpy support
+    ('Python', '3.11.5'),
+    ('cURL', '8.3.0'),
+    ('NSS', '3.94'),    # provides libfreebl3
+    ('SciPy-bundle', '2023.11'),    # optional, for numpy support
 ]
 
 use_pip = True