environment.yml

name: cphasing
channels:
- conda-forge
- bioconda
- anaconda
- nodefaults
dependencies:
- python 3.12.0.*
- rich-click 1.7.4.*
- biopython >=1.84,<2
- click-didyoumean >=0.3.1,<0.4
- colormaps >=0.4.2,<0.5
- dask >=2024.11.2,<2025
- pyranges >=0.1.2,<0.2
- joblib >=1.4.2,<2
- pandarallel >=1.6.5,<2
- natsort >=8.4.0,<9
- ncls >=0.0.68,<0.0.69
- cooler >=0.10.2,<0.11
- msgspec >=0.18.6,<0.19
- pandas >=2.2.3,<3
- numpy >=1.26.4,<2
- polars >=1.17.1,<1.18.0
- portion >=2.5.0,<3
- patchworklib >=0.6.3,<0.7
- python-igraph >=0.11.8,<0.12
- networkx >=3.4.2,<4
- pyarrow >=18.1.0,<19
- intervaltree >=3.1.0,<4
- hicmatrix >=17.2,<18
- seaborn >=0.13.2,<0.14
- scikit-learn >=1.5.2,<2
- pytools >=2024.1.18,<2025
- pysam >=0.22.1,<0.23
- minimap2 >=2.28,<3
- chromap >=0.2.7,<0.3
- bedtools >=2.31.1,<3
- seqkit >=2.9.0,<3
- samtools >=1.21,<2
- pigz >=2.8,<3
- wfmash 0.17.0.*
- matplotlib >=3.9.3,<4
- line_profiler >=4.1.3,<5
- crabz >=0.9.0,<0.10