9e75f44f1a
Source-only snapshot of the cluster branch for WES execution. Large reference files (HPA/MANE/ensemble FASTA, model weights, ~597 MB) are omitted: they are baked into the container images at build time and mounted from the dreamdock-data PVC at runtime, and exceed the Gitea request size limit. Pipeline entry point is main.nf, which orchestrates the biotransformer, conplex and tissue modules as a single workflow. Ligand inputs are read from the eureka workspace; protein_zarr and chembl_db come from the dreamdock-data PVC.
72 lines
2.5 KiB
Plaintext
Executable File
72 lines
2.5 KiB
Plaintext
Executable File
FROM debian:bullseye-slim
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USER root
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SHELL ["/bin/bash", "-c"]
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WORKDIR /home
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RUN mkdir -p /home/omic
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WORKDIR /home/omic
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ARG DEBIAN_FRONTEND=noninteractive
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RUN apt update -y && apt-get install -y --no-install-recommends \
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build-essential \
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cmake \
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curl \
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git \
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wget \
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ca-certificates \
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default-jre \
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unzip \
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&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/*
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RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh \
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&& bash miniconda.sh -b -p /opt/conda \
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&& rm miniconda.sh \
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&& ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh \
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&& echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc \
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&& echo "conda activate base" >> ~/.bashrc \
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&& find /opt/conda/ -follow -type f -name '*.a' -delete \
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&& find /opt/conda/ -follow -type f -name '*.js.map' -delete \
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&& /opt/conda/bin/conda clean -afy
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ENV PATH /opt/conda/bin:$PATH
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# main conda env (biotransformer)
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RUN conda create -n biotransformer
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ENV PATH="$PATH:/opt/conda/envs/biotransformer/bin"
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RUN echo "source activate biotransformer" >> ~/.bashrc
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RUN conda clean --all -f -y
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# Install RDKit
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RUN conda install -y -n biotransformer -c conda-forge rdkit
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WORKDIR /home/omic
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# RUN wget https://bitbucket.org/wishartlab/biotransformer3.0jar/get/6432cf887ed7.zip && \
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# unzip 6432cf887ed7.zip && \
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# rm 6432cf887ed7.zip && \
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# mv wishartlab-biotransformer3.0jar-6432cf887ed7 biotransformer
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# RUN git clone https://github.com/Wishartlab-openscience/Biotransformer.git && \
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# mv Biotransformer biotransformer
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RUN git clone https://bitbucket.org/wishartlab/biotransformer3.0jar biotransformer && mv biotransformer/BioTransformer3.0_20230525.jar biotransformer/biotransformer
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WORKDIR /home/omic/biotransformer
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# RUN wget https://bitbucket.org/wishartlab/biotransformer3.0jar/raw/6432cf887ed70c7c943c2dfeb60298ccdc788d7d/BioTransformer3.0_20230525.jar && \
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# mv BioTransformer3.0_20230525.jar biotransformer && \
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# chmod +x biotransformer
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ENV PATH="$PATH:/home/omic/biotransformer"
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# Create a symlink from /home/omic/biotransformer/database to /home/omic/biotransformer/btkb
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RUN ln -s /home/omic/biotransformer/database /home/omic/biotransformer/btkb
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## Test
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# RUN java -jar biotransformer -multiThread "2 example.csv 36000 3 1 true"
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#Download The Human Metabolome Database smiles
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RUN wget https://hmdb.ca/system/downloads/current/structures.zip
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RUN unzip structures.zip
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#install pandas and requests
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RUN conda install -y -n biotransformer -c conda-forge pandas requests
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