Open samnooij opened 2 months ago
I tried another conda environment, created by my colleague, and it works! The CCTyper version is also 1.8.0, but the Python and required library versions are different:
Package | not working version | working version |
---|---|---|
Python | 3.8.19 | 3.8.13 |
numpy | 1.24.4 | 1.23.4 |
pandas | 2.0.3 | 1.5.1 |
scipy | 1.10.1 | 1.9.3 |
biopython | 1.83 | 1.79 |
multiprocess | 0.70.16 | 0.70.14 |
scikit-learn | 1.3.2 | 1.1.3 |
py-xgboost | 2.1.1 | 1.7.1 |
tqdm | 4.66.5 | 4.64.1 |
Now since the warnings are from xgboost
and biopython
I suppose downgrading those two should fix it for now. Maybe the conda recipe can be updated with max versions?
-- edit:
Indeed, it works with the conda YAML file below! I only get the pkg_resources is deprecated
warning message now.
name: cctyper
dependencies:
- cctyper=1.8.0
- biopython=1.79
- libxgboost=1.7.1
- py-xgboost=1.7.1
channels:
- conda-forge
- bioconda
- russel88
I just installed CCTyper through conda/mamba and unfortunately it won't run at all. To be precise, I ran the command
mamba env create -f cctyper.yaml
and the contents ofcctyper.yaml
are pasted below.After installing, I activated the environment, and ran
cctyper --help
or justcctyper
, which returns the error:Besides that, I'm getting two deprecation warnings: one that pkg_resources is deprecated (https://setuptools.pypa.io/en/latest/pkg_resources.html) and one that Biopython's Bio.pairwise2 is deprecated and may be replaced by Bio.Align.PairwiseAligner. I'm running Ubuntu 22.04.4 LTS. Any idea how to solve this? Thanks in advance!
-- update 2024-09-13 I just tried versions 1.7.1 and 1.6.4 using the same installation method, and I get the exact same problem.