I encountered a few problems when installing and the following is my solution.
My setup: CentOS7 + micromamba
When python version not specified, micromamba automatically downloads the latest python=3.14, which is incompatible with pyrodigal. Also the newer version of biopython appears to have deleted the function get_amino_acids_percent. I had to downgrade python to 3.8 to successfully run the test run.
Also since I use CentOS7, pip does not work properly and I had to install all dependencies directly from conda
Recommended installation process:
conda create -n phager python=3.8
conda install --channel conda-forge pandas tqdm icecream colorama biopython more-itertools lightgbm scikit-learn pyarrow
conda install --channel bioconda pyrodigal
git clone https://github.com/ku-cbd/phager.git
cd phager
I encountered a few problems when installing and the following is my solution.
My setup: CentOS7 + micromamba
When python version not specified, micromamba automatically downloads the latest python=3.14, which is incompatible with pyrodigal. Also the newer version of biopython appears to have deleted the function
get_amino_acids_percent. I had to downgrade python to 3.8 to successfully run the test run.Also since I use CentOS7,
pipdoes not work properly and I had to install all dependencies directly from condaRecommended installation process: