From e55060d2d37737013c6fc480486605433a4f730c Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Mon, 16 Dec 2024 18:39:25 +0100
Subject: [PATCH] #473 working pre-PR version

---
 473_ChewBBACA/chewBBACA.eb | 94 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 94 insertions(+)
 create mode 100644 473_ChewBBACA/chewBBACA.eb

diff --git a/473_ChewBBACA/chewBBACA.eb b/473_ChewBBACA/chewBBACA.eb
new file mode 100644
index 0000000..c3fb1dc
--- /dev/null
+++ b/473_ChewBBACA/chewBBACA.eb
@@ -0,0 +1,94 @@
+easyblock = 'PythonBundle'
+
+name = 'chewBBACA'
+version = '3.3.10'
+
+homepage = 'https://github.com/B-UMMI/chewBBACA'
+description = """
+chewBBACA is a software suite for the creation and evaluation of core genome and
+whole genome MultiLocus Sequence Typing (cg/wgMLST) schemas and results.
+The "BBACA" stands for "BSR-Based Allele Calling Algorithm".
+BSR stands for BLAST Score Ratio as proposed by Rasko DA et al.
+The "chew" part adds extra coolness to the name and could be thought of as
+"Comprehensive and Highly Efficient Workflow"."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+# DEPS:
+    # OK "numpy~=1.24.3",
+    # OK "scipy~=1.10.1",
+    # OK "biopython>=1.79",
+    # OK "plotly>=5.8.0",
+    # ok "SPARQLWrapper>=2.0.0",
+    # OK "pandas>=1.5.1,<2.1",
+    # OK "requests>=2.27.1",
+    # ok "pyrodigal>=3.0.0"
+    # OK BLAST >=2.9.0 (we recommend using BLAST 2.9.0+)
+    # NO - not need Prodigal >=2.6.3 (for chewBBACA <3.3.0)
+    # OK MAFFT >=7.505 (for schema evaluation only)
+    # OK FastTree >=2.1.11 (for allele calling evaluation only)
+    # OK pyrodigal 3.6.3 requires archspec, which is not installed.
+    # OK chewbbaca 3.3.10 has requirement numpy~=1.24.3, but you have numpy 1.25.1.
+    # OK chewbbaca 3.3.10 has requirement scipy~=1.10.1, but you have scipy 1.11.1.
+
+builddependencies = [
+    ('scikit-build-core', '0.9.3'),
+    ('poetry', '1.5.1'),
+]
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('Biopython', '1.83'),
+    ('plotly.py', '5.16.0'),
+    ('Cython', '3.0.7'),
+    ('BLAST+', '2.14.1'),
+    ('MAFFT', '7.520', '-with-extensions'),
+    ('FastTree', '2.1.11'),
+    ('archspec', '0.2.1'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+local_preinstallopts = ("sed -i "
+"-e 's/numpy~=1.24.3/numpy>=1.24.3/g' "
+"-e 's/scipy~=1.10.1/scipy>=1.10.1/g' "
+'pyproject.toml && '
+)
+
+exts_list = [
+    ('pyrodigal', '3.6.3', {
+        'checksums': ['3e226f743c960d4d30c46ae6868aff7e2a6b98f8d837cfbd2637568569b21f78'],
+    }),
+    ('isodate', '0.6.1', {
+        'checksums': ['48c5881de7e8b0a0d648cb024c8062dc84e7b840ed81e864c7614fd3c127bde9'],
+    }),
+    ('rdflib', '7.1.1', {
+        'checksums': ['164de86bd3564558802ca983d84f6616a4a1a420c7a17a8152f5016076b2913e'],
+    }),
+    ('SPARQLWrapper', '2.0.0', {
+        'modulename': 'SPARQLWrapper',
+        'checksums': ['3fed3ebcc77617a4a74d2644b86fd88e0f32e7f7003ac7b2b334c026201731f1'],
+    }),
+    (name, version, {
+        'modulename': 'CHEWBBACA',
+        'sources': [SOURCELOWER_TAR_GZ],
+        'preinstallopts': local_preinstallopts,
+        'testinstall': True,
+        'runtest': "python setup.py test",
+        'checksums': ['f22cc90a3ac55c203669fc3d6647aabd4f939999c44ddd9d4d44881f7304cb0e'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/chewBBACA.py', 'bin/chewie'],
+    'dirs': [],
+}
+
+sanity_check_commands = [
+    'chewBBACA.py --help',
+    'chewie --help',
+]
+
+moduleclass = 'bio'