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Adding in all the work from the long-term Special Project Malaria bra…
…nch (#440) * Adding in all the work from the long-term Special Project Malaria branch
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| # Start with a good base python3 image: | ||
| FROM ubuntu:20.04 | ||
| MAINTAINER Jonn Smith <[email protected]> | ||
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| # Make sure we don't need to interact with any package installations: | ||
| ARG DEBIAN_FRONTEND=noninteractive | ||
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| # Set the working directory to / | ||
| WORKDIR / | ||
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| ################################################################################ | ||
| # Install system packages: | ||
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| # Make sure we can actually talk to package repos: | ||
| RUN apt-get update | ||
| RUN apt-get install -y apt-utils | ||
| RUN apt-get -y upgrade | ||
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| RUN apt-get update && apt-get -y upgrade | ||
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| # Development / prereqs for building software: | ||
| # Utilities / tools: | ||
| # Get libcurses: | ||
| # install gsutil requirements: | ||
| RUN apt-get -y install make gcc g++ autoconf sudo && \ | ||
| apt-get -y install git bash vim time bc sed perl wget curl bzip2 man unzip && \ | ||
| apt-get -y install liblzma-dev libbz2-dev libncurses5-dev libncursesw5-dev && \ | ||
| apt-get --allow-releaseinfo-change update && \ | ||
| apt install -y curl git-lfs time datamash | ||
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| # Install python: | ||
| RUN apt-get install -y python python3 python3-pip | ||
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| # Setup crcmodc for gsutil: | ||
| RUN apt-get install -y gcc python3-dev python3-setuptools && \ | ||
| pip3 uninstall -y crcmod && \ | ||
| pip3 install --no-cache-dir -U crcmod | ||
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| # install gsutil: | ||
| RUN curl https://sdk.cloud.google.com | bash | ||
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| # Get Java: | ||
| # Install OpenJDK-8 | ||
| RUN apt-get update && \ | ||
| apt-get install -y openjdk-11-jdk && \ | ||
| apt-get install -y ant && \ | ||
| apt-get clean | ||
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| # Fix certificate issues | ||
| RUN apt-get update && \ | ||
| apt-get install ca-certificates-java && \ | ||
| apt-get clean && \ | ||
| update-ca-certificates -f | ||
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| # Setup JAVA_HOME -- useful for docker commandline | ||
| ENV JAVA_HOME /usr/lib/jvm/java-11-openjdk-amd64/ | ||
| RUN export JAVA_HOME | ||
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| # Get snPEff | ||
| RUN wget https://snpeff.blob.core.windows.net/versions/snpEff_latest_core.zip && \ | ||
| unzip snpEff_latest_core.zip | ||
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| # Get tabix (for bgzip): | ||
| RUN apt-get install -y tabix | ||
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| ################################################################################ | ||
| # Final runtime configuration: | ||
| # Let's start at the root: | ||
| WORKDIR / | ||
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| IMAGE_NAME = lr-functional-annotation | ||
| VERSION = 0.0.1 | ||
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| TAG1 = us.gcr.io/broad-dsp-lrma/$(IMAGE_NAME):$(VERSION) | ||
| TAG2 = us.gcr.io/broad-dsp-lrma/$(IMAGE_NAME):latest | ||
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| all: | build push | ||
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| build: | ||
| docker build -t $(TAG1) -t $(TAG2) . | ||
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| build_no_cache: | ||
| docker build --no-cache -t $(TAG1) -t $(TAG2) . | ||
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| push: | ||
| docker push $(TAG1) | ||
| docker push $(TAG2) |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,33 @@ | ||
| FROM continuumio/miniconda3:22.11.1 | ||
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| MAINTAINER Jonn Smith | ||
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| # Set the resolver to libmamba: | ||
| RUN conda update -y -n base conda && \ | ||
| conda install -y -c conda-forge conda-pack libmamba && \ | ||
| conda config --set solver libmamba && \ | ||
| conda clean --all --yes | ||
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| # copy other resources | ||
| COPY ./environment.yml / | ||
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| # install conda packages | ||
| RUN conda env create -f /environment.yml && conda clean -a | ||
| ENV PATH=/root/google-cloud-sdk/bin/:${PATH} | ||
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| # install gsutil | ||
| RUN apt-get --allow-releaseinfo-change update | ||
| RUN apt install -y curl git-lfs time datamash | ||
| RUN curl https://sdk.cloud.google.com | bash | ||
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| # Setup crcmodc for gsutil: | ||
| RUN apt-get install -y gcc python3-dev python3-setuptools && \ | ||
| pip3 uninstall -y crcmod && \ | ||
| pip3 install --no-cache-dir -U crcmod | ||
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| # copy python scripts | ||
| COPY python/* /python_scripts/ | ||
| RUN chmod +x /python_scripts/* | ||
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| # activate conda environment | ||
| RUN echo "source activate lr-malaria" > ~/.bashrc |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,17 @@ | ||
| IMAGE_NAME = lr-malaria | ||
| VERSION = 0.0.1 | ||
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| TAG1 = us.gcr.io/broad-dsp-lrma/$(IMAGE_NAME):$(VERSION) | ||
| TAG2 = us.gcr.io/broad-dsp-lrma/$(IMAGE_NAME):latest | ||
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| all: | build push | ||
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| build: | ||
| docker build -t $(TAG1) -t $(TAG2) . | ||
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| build_no_cache: | ||
| docker build --no-cache -t $(TAG1) -t $(TAG2) . | ||
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| push: | ||
| docker push $(TAG1) | ||
| docker push $(TAG2) |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,22 @@ | ||
| name: lr-malaria | ||
| channels: | ||
| - default | ||
| - bioconda | ||
| - anaconda | ||
| dependencies: | ||
| - python=3.6 | ||
| - cython | ||
| - pip | ||
| - pip: | ||
| - numpy | ||
| - scipy | ||
| - pandas | ||
| - seaborn | ||
| - statsmodels | ||
| - networkx | ||
| - matplotlib | ||
| - patsy | ||
| - openpyxl | ||
| - scikit-learn | ||
| - numpyencoder | ||
| - tqdm |
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