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'