Docker build fails due to conda conflicts

[p1nkuu]

Hello,

I was trying to run the four commands given on the README to install the model in WSL but I encountered an error running conda env create -f biomedgpt.yml so I tried using the Dockerfile and encountered the same error building the Docker image, for the command RUN conda env update -f biomedgpt.yml.

UnsatisfiableError: The following specifications were found to be incompatible with a past
explicit spec that is not an explicit spec in this operation (python):

- certifi==2022.9.24=py37h06a4308_0 -> python[version='>=3.7,<3.8.0a0']
- pip -> python[version='>=2.7,<2.8.0a0|>=3.10,<3.11.0a0|>=3.11,<3.12.0a0|>=3.12,<3.13.0a0|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0|>=3.8,<3.9.0a0|>=3.9,<3.10.0a0']
- setuptools==65.5.0=py37h06a4308_0 -> python[version='>=3.7,<3.8.0a0']
- wheel==0.37.1=pyhd3eb1b0_0 -> python

The following specifications were found to be incompatible with each other:

Package wheel conflicts for:
pip -> wheel
Package openssl conflicts for:
python==3.7.4=h265db76_1 -> openssl[version='>=1.1.1c,<1.1.2a']
Package ncurses conflicts for:
readline==7.0=h7b6447c_5 -> ncurses[version='>=6.1,<7.0a0']
sqlite==3.33.0=h62c20be_0 -> ncurses[version='>=6.2,<7.0a0']
libedit==3.1.20210910=h7f8727e_0 -> ncurses[version='>=6.3,<7.0a0']
python==3.7.4=h265db76_1 -> ncurses[version='>=6.1,<7.0a0']
Package zlib conflicts for:
tk==8.6.12=h1ccaba5_0 -> zlib[version='>=1.2.12,<1.3.0a0']
python==3.7.4=h265db76_1 -> zlib[version='>=1.2.11,<1.3.0a0']
sqlite==3.33.0=h62c20be_0 -> zlib[version='>=1.2.11,<1.3.0a0']
Package libgcc-ng conflicts for:
python==3.7.4=h265db76_1 -> libgcc-ng[version='>=7.3.0']
ncurses==6.3=h5eee18b_3 -> libgcc-ng[version='>=11.2.0']
zlib==1.2.13=h5eee18b_0 -> libgcc-ng[version='>=11.2.0']
xz==5.2.8=h5eee18b_0 -> libgcc-ng[version='>=11.2.0']
sqlite==3.33.0=h62c20be_0 -> libgcc-ng[version='>=7.3.0']
openssl==1.1.1s=h7f8727e_0 -> libgcc-ng[version='>=7.5.0']
readline==7.0=h7b6447c_5 -> libgcc-ng[version='>=7.3.0']
tk==8.6.12=h1ccaba5_0 -> libgcc-ng[version='>=7.5.0']
libffi==3.2.1=hf484d3e_1007 -> libgcc-ng[version='>=7.3.0']
libedit==3.1.20210910=h7f8727e_0 -> libgcc-ng[version='>=7.5.0']
Package readline conflicts for:
python==3.7.4=h265db76_1 -> readline[version='>=7.0,<8.0a0']
Package __glibc conflicts for:
libgcc-ng==11.2.0=h1234567_1 -> __glibc[version='>=2.17']
libstdcxx-ng==11.2.0=h1234567_1 -> __glibc[version='>=2.17']
Package libstdcxx-ng conflicts for:
libffi==3.2.1=hf484d3e_1007 -> libstdcxx-ng[version='>=7.3.0']
python==3.7.4=h265db76_1 -> libstdcxx-ng[version='>=7.3.0']
Package pip conflicts for:
python==3.7.4=h265db76_1 -> pip
Package setuptools conflicts for:
pip -> setuptools
Package libgomp conflicts for:
libgcc-ng==11.2.0=h1234567_1 -> libgomp==11.2.0=h1234567_1
_openmp_mutex==5.1=1_gnu -> libgomp[version='>=7.5.0']
Package tk conflicts for:
python==3.7.4=h265db76_1 -> tk[version='>=8.6.8,<8.7.0a0']
Package _libgcc_mutex conflicts for:
libgomp==11.2.0=h1234567_1 -> _libgcc_mutex==0.1=main
libgcc-ng==11.2.0=h1234567_1 -> _libgcc_mutex==0.1=main
_openmp_mutex==5.1=1_gnu -> _libgcc_mutex==0.1=main
Package ca-certificates conflicts for:
openssl==1.1.1s=h7f8727e_0 -> ca-certificates
Package _openmp_mutex conflicts for:
libgcc-ng==11.2.0=h1234567_1 -> _openmp_mutex
Package sqlite conflicts for:
python==3.7.4=h265db76_1 -> sqlite[version='>=3.29.0,<4.0a0']
Package xz conflicts for:
python==3.7.4=h265db76_1 -> xz[version='>=5.2.4,<6.0a0']
Package libedit conflicts for:
sqlite==3.33.0=h62c20be_0 -> libedit[version='>=3.1.20191231,<3.2.0a0']
Package openmp_impl conflicts for:
_openmp_mutex==5.1=1_gnu -> openmp_impl==9999
Package certifi conflicts for:
setuptools==65.5.0=py37h06a4308_0 -> certifi[version='>=2016.9.26']
Package libffi conflicts for:
python==3.7.4=h265db76_1 -> libffi[version='>=3.2.1,<3.3a0']
Warning: you have pip-installed dependencies in your environment file, but you do not list pip itself as one of your conda dependencies.  Conda may not use the correct pip to install your packages, and they may end up in the wrong place.  Please add an explicit pip dependency.  I'm adding one for you, but still nagging you.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working...
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed 

Thanks

[taokz]

Could you re-install the environment using the following command:

cd BiomedGPT/
conda create --name biomedgpt python=3.7.4
conda activate biomedgpt
python -m pip install pip==21.2.4
pip install -r requirements.txt

If it does not work, please let me know.