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raven_assembler updated with docker image (#9)
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{ | ||
"images": { | ||
"raven": "docker://asyakhleborodova/raven_assembly:v0.1.0" | ||
} | ||
} |
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FROM ubuntu:22.04 | ||
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RUN mkdir -p /opt2 && mkdir -p /data2 | ||
WORKDIR /opt2 | ||
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# Set time zone to US east coast | ||
ENV TZ=America/New_York | ||
RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime \ | ||
&& echo $TZ > /etc/timezone | ||
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RUN apt-get update \ | ||
&& apt-get -y upgrade \ | ||
&& DEBIAN_FRONTEND=noninteractive apt-get install -y \ | ||
build-essential \ | ||
cmake \ | ||
curl \ | ||
gawk \ | ||
git \ | ||
gzip \ | ||
g++ \ | ||
libboost-dev \ | ||
libcurl4-openssl-dev \ | ||
libssl-dev \ | ||
libxml2-dev \ | ||
locales \ | ||
# python/3.10.6 | ||
python3 \ | ||
python3-pip \ | ||
samtools \ | ||
wget \ | ||
zlib1g-dev \ | ||
&& apt-get clean && apt-get purge \ | ||
&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* | ||
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ENV CONDA_DIR /opt2/conda | ||
RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh && \ | ||
/bin/bash ~/miniconda.sh -b -p /opt2/conda | ||
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# Put conda in path so we can use conda activate | ||
ENV PATH=$CONDA_DIR/bin:$PATH | ||
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# Set the locale | ||
RUN localedef -i en_US -f UTF-8 en_US.UTF-8 | ||
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############### INSTALL ################ | ||
RUN ln -sf /usr/bin/python3 /usr/bin/python | ||
RUN pip3 install --upgrade pip \ | ||
&& pip3 install matplotlib \ | ||
&& pip3 install numpy \ | ||
&& pip3 install pandas \ | ||
&& pip3 install scipy | ||
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RUN conda install -y --channel=defaults --channel=bioconda --channel=conda-forge raven-assembler | ||
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WORKDIR /opt2 | ||
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COPY Dockerfile /opt2 | ||
WORKDIR /data2 |
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## Steps for Building Docker Images | ||
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Directly below are instructions for building an image using the provided Dockerfile: | ||
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```bash | ||
# See listing of images on computer | ||
docker image ls | ||
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# Build from Dockerfile | ||
docker build --no-cache -f Dockerfile --tag=raven_assembly:v0.1.0 . | ||
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# Testing, take a peek inside | ||
docker run -ti raven_assembly:v0.1.0 /bin/bash | ||
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# Updating Tag before pushing to DockerHub | ||
docker tag raven_assembly:v0.1.0 asyakhleborodova/raven_assembly:v0.1.0 | ||
docker tag raven_assembly:v0.1.0 asyakhleborodova/raven_assembly # latest | ||
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# Check out new tag(s) | ||
docker image ls | ||
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# Push new tagged image to DockerHub | ||
docker push asyakhleborodova/raven_assembly:v0.1.0 | ||
docker push asyakhleborodova/raven_assembly:latest | ||
``` | ||
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### Other Recommended Steps | ||
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Scan your image for known vulnerabilities: | ||
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```bash | ||
docker scan raven_assembly:v0.1.0 | ||
``` | ||
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> **Please Note**: Any references to `asyakhleborodova` should be replaced your username if you would also like to push the image to a non-org account. |
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