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FROM ubuntu:18.04
MAINTAINER Jimin Park, [email protected]
# update and install dependencies
RUN apt-get update && \
apt-get -y install time git make wget autoconf gcc g++ vim sudo build-essential bzip2 zlib1g-dev libbz2-dev \
libcurl4-gnutls-dev liblzma-dev libncurses5-dev libncursesw5-dev libssl-dev
RUN mkdir -p /home/apps
### samtools
ARG SAMTOOLS_VERSION=1.17
RUN cd /home/apps && \
wget https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VERSION}/samtools-${SAMTOOLS_VERSION}.tar.bz2 && \
tar -vxjf samtools-${SAMTOOLS_VERSION}.tar.bz2 && \
rm -rf samtools-${SAMTOOLS_VERSION}.tar.bz2 && \
cd samtools-${SAMTOOLS_VERSION} && \
make
ENV PATH="/home/apps/samtools-${SAMTOOLS_VERSION}:$PATH"
### htslib
ARG HTSLIB_VERSION=1.17
RUN cd /home/apps && \
wget https://github.com/samtools/htslib/releases/download/${HTSLIB_VERSION}/htslib-${HTSLIB_VERSION}.tar.bz2 && \
tar -vxjf htslib-${HTSLIB_VERSION}.tar.bz2 && \
rm -rf htslib-${HTSLIB_VERSION}.tar.bz2 && \
cd htslib-${HTSLIB_VERSION} && \
make
ENV PATH="/home/apps/htslib-${HTSLIB_VERSION}:$PATH"
### bcftools
ARG BCFTOOLS_VERSION=1.17
RUN cd /home/apps && \
wget https://github.com/samtools/bcftools/releases/download/${BCFTOOLS_VERSION}/bcftools-${BCFTOOLS_VERSION}.tar.bz2 && \
tar -vxjf bcftools-${BCFTOOLS_VERSION}.tar.bz2 && \
rm -rf bcftools-${BCFTOOLS_VERSION}.tar.bz2 && \
cd bcftools-${BCFTOOLS_VERSION}/ && \
make
ENV PATH="/home/apps/bcftools-${BCFTOOLS_VERSION}:$PATH"
### minimap2
ARG MINIMAP2_VERSION=2.26
RUN cd /home/apps && \
wget https://github.com/lh3/minimap2/releases/download/v${MINIMAP2_VERSION}/minimap2-${MINIMAP2_VERSION}.tar.bz2 && \
tar -vxjf minimap2-${MINIMAP2_VERSION}.tar.bz2 && \
rm minimap2-${MINIMAP2_VERSION}.tar.bz2 && \
cd minimap2-${MINIMAP2_VERSION} && \
make
ENV PATH="/home/apps/minimap2-${MINIMAP2_VERSION}:$PATH"
### bwa-mem2
ARG BWA_MEM_VERSION=2.2.1
RUN cd /home/apps && \
apt-get -y update && apt-get -y install bzip2 && apt-get -y install curl && \
curl -L https://github.com/bwa-mem2/bwa-mem2/releases/download/v${BWA_MEM_VERSION}/bwa-mem2-${BWA_MEM_VERSION}_x64-linux.tar.bz2 | tar jxf - && \
rm -rf bwa-mem2-${BWA_MEM_VERSION}_x64-linux.tar.bz2
ENV PATH="/home/apps/bwa-mem2-2.2.1_x64-linux:$PATH"