Remove cctbx from dependencies

KosinskiLab · Oct 2, 2024 · 5a88e1e · 5a88e1e
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diff --git a/.github/workflows/github_actions.yml b/.github/workflows/github_actions.yml
@@ -32,7 +32,7 @@ jobs:
           echo "$GITHUB_WORKSPACE/alphapulldown" >> $GITHUB_PATH
       - if: matrix.install-type == 'user'
         run: |
-          conda create -n AlphaPulldown -c omnia -c bioconda -c conda-forge python==${{ matrix.python-version }} openmm==8.0 pdbfixer==1.9 kalign2 cctbx-base pytest importlib_metadata modelcif
+          conda create -n AlphaPulldown -c omnia -c bioconda -c conda-forge python==${{ matrix.python-version }} openmm==8.0 pdbfixer==1.9 kalign2 pytest importlib_metadata modelcif
           eval "$(conda shell.bash hook)"
           conda activate AlphaPulldown
           conda install -c bioconda hmmer hhsuite

diff --git a/README.md b/README.md
@@ -382,7 +382,7 @@ AlphaPulldown can be used as a set of scripts for every particular step.
 **Firstly**, install [Anaconda](https://www.anaconda.com/) and create an AlphaPulldown environment, gathering necessary dependencies:
 
 ```bash
-conda create -n AlphaPulldown -c omnia -c bioconda -c conda-forge python==3.10 openmm==8.0 pdbfixer==1.9 kalign2 cctbx-base pytest importlib_metadata hhsuite modelcif
+conda create -n AlphaPulldown -c omnia -c bioconda -c conda-forge python==3.10 openmm==8.0 pdbfixer==1.9 kalign2 pytest importlib_metadata hhsuite modelcif
 ```
        
 **Optionally**, if you do not have it yet on your system, install [HMMER](http://hmmer.org/documentation.html) from Anaconda:

diff --git a/docker/pulldown.dockerfile b/docker/pulldown.dockerfile
@@ -60,7 +60,6 @@ RUN conda install -y -c conda-forge -c bioconda --solver classic \
       openmm==8.0 \
       cudatoolkit==${CUDA_VERSION} \
       pdbfixer==1.9 \
-      cctbx-base \
       kalign2 \
       importlib_metadata \
       modelcif \