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environment.yml conda env has conflicts #188

Description

@Emptyset110

conda env create --name=fastfold -f environment.yml
shows lots of conflicts

Package xorg-libx11 conflicts for:
conda-forge::python=3.8 -> pypy3.8=7.3.11 -> xorg-libx11[version='>=1.8.4,<2.0a0|>=1.8.6,<2.0a0']
pytorch::torchvision -> ffmpeg[version='>=4.2'] -> xorg-libx11[version='>=1.8.7,<2.0a0']

Package pytorch conflicts for:
pytorch::torchaudio -> pytorch[version='1.10.0|1.10.1|1.10.2|1.11.0|1.12.0|1.12.1|1.13.0|1.13.1|2.0.0|2.0.1|2.1.0|2.1.1|2.1.2|2.2.0|1.9.1|1.9.0|1.8.1|1.8.0|1.7.1|1.7.0|1.6.0|1.5.1']
pytorch::pytorch=1.12
pytorch|pytorch::pytorch=1.12
pytorch::torchvision -> pytorch[version='1.10.0|1.10.1|1.10.2|1.11.0|1.12.0|1.12.1|1.13.0|1.13.1|2.0.0|2.0.1|2.1.0|2.1.1|2.1.2|2.2.0|1.9.1|1.9.0|1.8.1|1.8.0|1.7.1|1.7.0|1.6.0|1.5.1']

Package pytorch-cuda conflicts for:
pytorch::torchaudio -> pytorch==2.2.0 -> pytorch-cuda[version='>=11.6,<11.7|>=11.7,<11.8|>=11.8,<11.9|>=12.1,<12.2']
pytorch::torchaudio -> pytorch-cuda[version='11.6.*|11.7.*|11.8.*|12.1.*']

Package certifi conflicts for:
conda-forge::pip -> setuptools -> certifi[version='>=2016.09|>=2016.9.26']
pytorch::torchvision -> requests -> certifi[version='>=2017.4.17']
conda-forge::pdbfixer -> setuptools -> certifi[version='>=2016.09|>=2016.9.26']

Package ca-certificates conflicts for:
bioconda::hhsuite==3.3.0 -> python[version='>=2.7,<2.8.0a0'] -> ca-certificates
conda-forge::pip -> python -> ca-certificates
conda-forge::python=3.8 -> openssl[version='>=3.2.0,<4.0a0'] -> ca-certificates

Package openmm conflicts for:
conda-forge::openmm=7.7.0
conda-forge::pdbfixer -> openmm[version='>=7.5|>=7.6|>=8.0']The following specifications were found to be incompatible with your system:

  - feature:/linux-64::__cuda==12.3=0
  - feature:/linux-64::__glibc==2.31=0
  - feature:|@/linux-64::__cuda==12.3=0
  - feature:|@/linux-64::__glibc==2.31=0
  - bioconda::hhsuite==3.3.0 -> libgcc-ng[version='>=10.3.0'] -> __glibc[version='>=2.17']
  - bioconda::hmmer==3.3.2 -> libgcc-ng[version='>=10.3.0'] -> __glibc[version='>=2.17']
  - bioconda::kalign2==2.04 -> libgcc-ng[version='>=10.3.0'] -> __glibc[version='>=2.17']
  - conda-forge::cudatoolkit=11.3 -> __glibc[version='>=2.17,<3.0.a0']
  - conda-forge::cudatoolkit=11.3 -> libgcc-ng[version='>=10.3.0'] -> __glibc[version='>=2.17']
  - conda-forge::pdbfixer -> openmm[version='>=8.0'] -> __glibc[version='>=2.17|>=2.17,<3.0.a0']
  - conda-forge::python=3.8 -> libgcc-ng[version='>=10.3.0'] -> __glibc[version='>=2.17']
  - pytorch::pytorch=1.12 -> cudatoolkit[version='>=11.3,<11.4'] -> __glibc[version='>=2.17,<3.0.a0']
  - pytorch::torchaudio -> pytorch==2.1.2 -> __cuda[version='>=11.8']
  - pytorch::torchaudio -> pytorch==2.1.2 -> __glibc[version='>=2.17|>=2.17,<3.0.a0']
  - pytorch::torchvision -> pytorch==2.1.2 -> __cuda[version='>=11.8']
  - pytorch::torchvision -> pytorch==2.1.2 -> __glibc[version='>=2.17|>=2.17,<3.0.a0']

Your installed version is: 2.31

Note that strict channel priority may have removed packages required for satisfiability.

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