From 9f51497cf07f4b4480a585310ec23a1355545582 Mon Sep 17 00:00:00 2001
From: fizwit <john@fuzzdog.com>
Date: Fri, 20 Dec 2024 16:20:40 -0800
Subject: [PATCH 1/2] {bio}[foss/2023b] CrossMap 0.7.3

---
 .../bx-python/bx-python-0.13.0-foss-2023b.eb  | 35 ++++++++++++++++
 .../c/CrossMap/CrossMap-0.7.3-foss-2023b.eb   | 41 +++++++++++++++++++
 .../p/pyBigWig/pyBigWig-0.3.23-gfbf-2023b.eb  | 29 +++++++++++++
 3 files changed, 105 insertions(+)
 create mode 100644 easybuild/easyconfigs/b/bx-python/bx-python-0.13.0-foss-2023b.eb
 create mode 100644 easybuild/easyconfigs/c/CrossMap/CrossMap-0.7.3-foss-2023b.eb
 create mode 100644 easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.23-gfbf-2023b.eb

diff --git a/easybuild/easyconfigs/b/bx-python/bx-python-0.13.0-foss-2023b.eb b/easybuild/easyconfigs/b/bx-python/bx-python-0.13.0-foss-2023b.eb
new file mode 100644
index 00000000000..2b6e52f1211
--- /dev/null
+++ b/easybuild/easyconfigs/b/bx-python/bx-python-0.13.0-foss-2023b.eb
@@ -0,0 +1,35 @@
+easyblock = 'PythonBundle'
+
+name = 'bx-python'
+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': '2023b'}
+
+dependencies = [
+    ('Python', '3.11.5'),
+    ('LZO', '2.10'),
+    ('SciPy-bundle', '2023.11'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('python-lzo', '1.15', {
+        'modulename': 'lzo',
+        'preinstallopts': "export PREFIX=$EBROOTLZO && ",
+        'checksums': ['a57aaa00c5c3a0515dd9f7426ba2cf601767dc19dc023d8b99d4a13b0a327b49'],
+    }),
+    ('bx_python', version, {
+        'modulename': 'bx',
+        'checksums': ['ce04696543367efc6b7995d9463efeda691b9a58f6f55a7bd831e642159b0644'],
+    }),
+]
+
+sanity_check_commands = ['bnMapper.py --help']
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/c/CrossMap/CrossMap-0.7.3-foss-2023b.eb b/easybuild/easyconfigs/c/CrossMap/CrossMap-0.7.3-foss-2023b.eb
new file mode 100644
index 00000000000..3c344ba96f5
--- /dev/null
+++ b/easybuild/easyconfigs/c/CrossMap/CrossMap-0.7.3-foss-2023b.eb
@@ -0,0 +1,41 @@
+easyblock = 'PythonPackage'
+
+name = 'CrossMap'
+version = '0.7.3'
+
+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': '2023b'}
+
+# 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', '3.11.5'),
+    ('bx-python', '0.13.0'),
+    ('pyBigWig', '0.3.23'),
+    ('Pysam', '0.22.0'),
+]
+
+use_pip = True
+download_dep_fail = True
+
+sanity_check_commands = [('CrossMap', '--help')]
+
+sanity_check_paths = {
+    'files': ['bin/CrossMap'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+options = {'modulename': 'cmmodule'}
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.23-gfbf-2023b.eb b/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.23-gfbf-2023b.eb
new file mode 100644
index 00000000000..25ea4ec30cc
--- /dev/null
+++ b/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.23-gfbf-2023b.eb
@@ -0,0 +1,29 @@
+easyblock = 'PythonPackage'
+
+name = 'pyBigWig'
+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': '2023b'}
+
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['b780c2b77f024c7967d7bd2eca0fa39a4d939c86b807135960e26faafafbec84']
+
+dependencies = [
+    ('Python', '3.11.5'),
+    ('cURL', '8.3.0'),
+    ('NSS', '3.94'),    # provides libfreebl3
+    ('SciPy-bundle', '2023.11'),    # optional, for numpy support
+]
+
+use_pip = True
+download_dep_fail = True
+
+options = {'modulename': name}
+
+sanity_pip_check = True
+
+moduleclass = 'bio'

From c30f0c800629d0fcfad680560796b248c8d94b54 Mon Sep 17 00:00:00 2001
From: fizwit <john@fuzzdog.com>
Date: Sat, 21 Dec 2024 14:03:23 -0800
Subject: [PATCH 2/2] sanity_pip_check

---
 easybuild/easyconfigs/c/CrossMap/CrossMap-0.7.3-foss-2023b.eb | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easybuild/easyconfigs/c/CrossMap/CrossMap-0.7.3-foss-2023b.eb b/easybuild/easyconfigs/c/CrossMap/CrossMap-0.7.3-foss-2023b.eb
index 3c344ba96f5..90210916e16 100644
--- a/easybuild/easyconfigs/c/CrossMap/CrossMap-0.7.3-foss-2023b.eb
+++ b/easybuild/easyconfigs/c/CrossMap/CrossMap-0.7.3-foss-2023b.eb
@@ -28,6 +28,7 @@ dependencies = [
 
 use_pip = True
 download_dep_fail = True
+sanity_pip_check = True
 
 sanity_check_commands = [('CrossMap', '--help')]