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FROM ubuntu:20.04
MAINTAINER Onur Yukselen <onur.yukselen@umassmed.edu>
ENV PATH="/bin:/sbin:/usr/bin/samtools-1.9:/usr/bin/sratoolkit.2.10.7-ubuntu64/bin:${PATH}"
RUN apt-get update
RUN apt-get -y upgrade
RUN apt-get dist-upgrade
RUN DEBIAN_FRONTEND=noninteractive apt-get -y install unzip libsqlite3-dev libbz2-dev libssl-dev python python-dev liblzma-dev \
git libxml2-dev software-properties-common wget tree vim sed make libncurses5-dev libncursesw5-dev\
subversion g++ gcc gfortran libcurl4-openssl-dev curl zlib1g-dev build-essential libffi-dev \
libxml-libxml-perl jq pip
RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-4.5.11-Linux-x86_64.sh -O ~/miniconda.sh && \
/bin/bash ~/miniconda.sh -b -p /opt/conda && \
rm ~/miniconda.sh && \
/opt/conda/bin/conda clean -tipsy && \
ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh && \
echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc && \
echo "conda activate base" >> ~/.bashrc
### SRA-toolkit
RUN mkdir -p /data /project /nl /share
RUN cd /usr/bin && wget https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.10.7/sratoolkit.2.10.7-ubuntu64.tar.gz && \
tar -xvzf sratoolkit.2.10.7-ubuntu64.tar.gz
### S3CMD
RUN apt-get -y upgrade
RUN apt-get -y install python-setuptools
RUN pip install s3cmd
RUN apt-get -y autoremove
### Samtools
RUN cd /usr/bin && wget https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2 && \
tar -vxjf samtools-1.9.tar.bz2 && cd samtools-1.9 && make
### AWS CLI
RUN apt-get update && apt-get install -y gcc unzip
RUN curl "https://awscli.amazonaws.com/awscli-exe-linux-x86_64-2.0.30.zip" -o "awscliv2.zip"
RUN unzip awscliv2.zip
RUN ./aws/install
RUN aws --version
### gcloud gsutils
RUN curl https://dl.google.com/dl/cloudsdk/release/google-cloud-sdk.tar.gz > /tmp/google-cloud-sdk.tar.gz
RUN mkdir -p /usr/local/gcloud \
&& tar -C /usr/local/gcloud -xvf /tmp/google-cloud-sdk.tar.gz \
&& /usr/local/gcloud/google-cloud-sdk/install.sh
ENV PATH $PATH:/usr/local/gcloud/google-cloud-sdk/bin
RUN echo "DONE!"