Running via docker is not working anymore

[adrianodemarino]

Before was working correctly but now when you run: docker run -v /Users/adriano/Documents/git/vcf2gwas/:/vcf2gwas/ fvogt257/vcf2gwas -v test you will get this error:

WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv
Traceback (most recent call last):
  File "/root/miniconda3/envs/python-app/lib/python3.9/site-packages/vcf2gwas/utils.py", line 69, in <module>
    import umap
ModuleNotFoundError: No module named 'umap'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/root/miniconda3/envs/python-app/lib/python3.9/site-packages/vcf2gwas/starter.py", line 23, in <module>
    from vcf2gwas.utils import *
  File "/root/miniconda3/envs/python-app/lib/python3.9/site-packages/vcf2gwas/utils.py", line 72, in <module>
    import umap
  File "/root/miniconda3/envs/python-app/lib/python3.9/site-packages/umap/__init__.py", line 2, in <module>
    from .umap_ import UMAP
  File "/root/miniconda3/envs/python-app/lib/python3.9/site-packages/umap/umap_.py", line 28, in <module>
    import numba
  File "/root/miniconda3/envs/python-app/lib/python3.9/site-packages/numba/__init__.py", line 55, in <module>
    _ensure_critical_deps()
  File "/root/miniconda3/envs/python-app/lib/python3.9/site-packages/numba/__init__.py", line 40, in _ensure_critical_deps
    raise ImportError(msg)
ImportError: Numba needs NumPy 1.21 or greater. Got NumPy 1.20.

vcf2gwas v0.8.8

Initialising..

Copying example input files to current working directory..
Copying README and LICENSE files..

The error occurs when the docker is preparing the env. Could you please share in the repo the docker file?, that will simplify things .

[samuelecancellieri]

I'm having the same issue, I think the problem is a conda package that got updated. can you share the docker file to help solve the problem? @frankvogt

[frankvogt]

I updated the dependencies and uploaded the new version, everything should work again. Additionally, the docker file can be found here.