diff --git a/Dockerfile b/Dockerfile index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..4c9c94124fffbb97a013682fcaa14da5489d66ec 100644 --- a/Dockerfile +++ b/Dockerfile @@ -0,0 +1,30 @@ +# base img +FROM condaforge/mambaforge:4.12.0-0 + +# add yaml config to /conf +ADD conda/ /conf/ + +# install basic dependencies +RUN apt-get update && \ + apt-get install -y curl wget && \ + rm -rf /var/lib/apt/lists/* + +# install seqdb +RUN seqdb_vers="1.0" && \ + wget https://github.com/jimmyliu1326/seqdb/archive/refs/tags/v${seqdb_vers}.tar.gz -O /seqdb.tar.gz && \ + tar -xzf /seqdb.tar.gz && \ + rm /seqdb.tar.gz && \ + echo "export PATH=/seqdb-${seqdb_vers}/:\$PATH" >> ~/.bashrc && \ + source ~/.bashrc + +# create a conda env for each yaml config +RUN CONDA_DIR="/opt/conda" && \ + for file in $(ls /conf); do mamba env create --file /conf/$file; done + +# clean up unused and cached pkgs +RUN CONDA_DIR="/opt/conda" && \ + mamba clean --all --yes && \ + rm -rf $CONDA_DIR/conda-meta && \ + rm -rf $CONDA_DIR/include && \ + rm -rf $CONDA_DIR/lib/python3.*/site-packages/pip && \ + find $CONDA_DIR -name '__pycache__' -type d -exec rm -rf '{}' '+' \ No newline at end of file