ERROR: Cannot install colabfold and tensorflow-cpu==2.11.0 because these package versions have conflicting dependencies.

Expected Behavior

To be able to. run ColabFold in the colab notebook with no issues.

Current Behavior

I get an error when trying to install dependencies.

Steps to Reproduce (for bugs)

Please make sure to reproduce the issue after a "Factory Reset" in Colab. If running locally ypdate you local installation colabfold_batch to the newest version. Please provide your input if you can share it.

ColabFold Output (for bugs)

Please make sure to also post the complete ColabFold output. You can use gist.github.com for large output. installing colabfold... ERROR: Cannot install colabfold and tensorflow-cpu==2.11.0 because these package versions have conflicting dependencies. ERROR: ResolutionImpossible: for help visit https://pip.pypa.io/en/latest/topics/dependency-resolution/#dealing-with-dependency-conflicts

CalledProcessError Traceback (most recent call last) in <cell line: 1>() ----> 1 get_ipython().run_cell_magic('bash', '-s $use_amber $use_templates $python_version', '\nset -e\n\nUSE_AMBER=$1\nUSE_TEMPLATES=$2\nPYTHON_VERSION=$3\n\nif [ ! -f COLABFOLD_READY ]; then\n echo "installing colabfold..."\n # install dependencies\n # We have to use "--no-warn-conflicts" because colab already has a lot preinstalled with requirements different to ours\n pip install -q --no-warn-conflicts "colabfold[alphafold-minus-jax] @ git+https://github.com/sokrypton/ColabFold" "tensorflow-cpu==2.11.0"\n pip uninstall -yq jax jaxlib\n pip install -q "jax[cuda]==0.3.25" -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html\n\n\n # for debugging\n ln -s /usr/local/lib/python3./dist-packages/colabfold colabfold\n ln -s /usr/local/lib/python3./dist-packages/alphafold alphafold\n touch COLABFOLD_READY\nfi\n\n# setup conda\nif [ ${USE_AMBER} == "True" ] || [ ${USE_TEMPLATES} == "True" ]; then\n if [ ! -f CONDA_READY ]; then\n echo "installing conda..."\n wget -qnc https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh\n bash Miniconda3-latest-Linux-x86_64.sh -bfp /usr/local 2>&1 1>/dev/null\n rm Miniconda3-latest-Linux-x86_64.sh\n touch CONDA_READY\n fi\nfi\n# setup template search\nif [ ${USE_TEMPLATES} == "True" ] && [ ! -f HH_READY ]; then\n echo "installing hhsuite..."\n conda install -...

4 frames /usr/local/lib/python3.10/dist-packages/google/colab/_shell.py in run_cell_magic(self, magic_name, line, cell) 332 if line and not cell: 333 cell = ' ' --> 334 return super().run_cell_magic(magic_name, line, cell) 335 336

/usr/local/lib/python3.10/dist-packages/IPython/core/interactiveshell.py in run_cell_magic(self, magic_name, line, cell) 2471 with self.builtin_trap: 2472 args = (magic_arg_s, cell) -> 2473 result = fn(*args, **kwargs) 2474 return result 2475

/usr/local/lib/python3.10/dist-packages/IPython/core/magics/script.py in named_script_magic(line, cell) 140 else: 141 line = script --> 142 return self.shebang(line, cell) 143 144 # write a basic docstring:

in shebang(self, line, cell) [/usr/local/lib/python3.10/dist-packages/IPython/core/magic.py](https://localhost:8080/#) in (f, *a, **k) 185 # but it's overkill for just that one bit of state. 186 def magic_deco(arg): --> 187 call = lambda f, *a, **k: f(*a, **k) 188 189 if callable(arg): [/usr/local/lib/python3.10/dist-packages/IPython/core/magics/script.py](https://localhost:8080/#) in shebang(self, line, cell) 243 sys.stderr.flush() 244 if args.raise_error and p.returncode!=0: --> 245 raise CalledProcessError(p.returncode, cell, output=out, stderr=err) 246 247 def _run_script(self, p, cell, to_close): CalledProcessError: Command 'b'\nset -e\n\nUSE_AMBER=$1\nUSE_TEMPLATES=$2\nPYTHON_VERSION=$3\n\nif [ ! -f COLABFOLD_READY ]; then\n echo "installing colabfold..."\n # install dependencies\n # We have to use "--no-warn-conflicts" because colab already has a lot preinstalled with requirements different to ours\n pip install -q --no-warn-conflicts "colabfold[alphafold-minus-jax] @ git+https://github.com/sokrypton/ColabFold" "tensorflow-cpu==2.11.0"\n pip uninstall -yq jax jaxlib\n pip install -q "jax[cuda]==0.3.25" -f [https://storage.googleapis.com/jax-releases/jax_cuda_releases.html\n\n\n](https://storage.googleapis.com/jax-releases/jax_cuda_releases.html/n/n/n) # for debugging\n ln -s /usr/local/lib/python3.*/dist-packages/colabfold colabfold\n ln -s /usr/local/lib/python3.*/dist-packages/alphafold alphafold\n touch COLABFOLD_READY\nfi\n\n# setup conda\nif [ ${USE_AMBER} == "True" ] || [ ${USE_TEMPLATES} == "True" ]; then\n if [ ! -f CONDA_READY ]; then\n echo "installing conda..."\n wget -qnc [https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh\n](https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh/n) bash Miniconda3-latest-Linux-x86_64.sh -bfp /usr/local 2>&1 1>/dev/null\n rm Miniconda3-latest-Linux-x86_64.sh\n touch CONDA_READY\n fi\nfi\n# setup template search\nif [ ${USE_TEMPLATES} == "True" ] && [ ! -f HH_READY ]; then\n echo "installing hhsuite..."\n conda install -y -q -c conda-forge -c bioconda kalign2=2.04 hhsuite=3.3.0 python="${PYTHON_VERSION}" 2>&1 1>/dev/null\n touch HH_READY\nfi\n# setup openmm for amber refinement\nif [ ${USE_AMB... ## Context Providing context helps us come up with a solution and improve our documentation for the future. I'm trying to run a pipeline for ab-ag docking which uses ColabFold. Since this is the first step (and it's failing) my pipeline is broken. ## Your Environment Include as many relevant details about the environment you experienced the bug in. * Git commit used * If you run it on a local system. Please add the server specifications * Operating system and version: I've tried running this on a school server, locally on my Mac M2 Pro, and in google colab and have not been able to.

sokrypton / ColabFold