hisat2-samtools1.5-convert

#基础镜像
#FROM alpine:latest
#维护者信息
MAINTAINER Yao Mengcheng <mengchengyao@genome.cn>
ENV LANG=en_US.UTF-8
## 配置清华镜像地址
RUN echo "https://mirror.tuna.tsinghua.edu.cn/alpine/v3.8/main/" > /etc/apk/repositories
## 设置时区变量
ENV TIME_ZONE Asia/Shanghai
## #安装时区包并配置时区TIME_ZONE为中国标准时间
RUN apk add --no-cache -U tzdata ;\
     ln -sf /usr/share/zoneinfo/${TIME_ZONE} /etc/localtime ;\
     echo "${TIME_ZONE}" > /etc/timezone
##安装imagemagick软件，主要是图片转换
RUN apk add --no-cache  imagemagick

####安装samtools 1.6版本的
ENV SAMTOOLS_VERSION 1.5
RUN apk add --no-cache build-base zlib-dev bzip2-dev xz-dev ncurses-dev ca-certificates wget; \
    wget -q https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VERSION}/samtools-${SAMTOOLS_VERSION}.tar.bz2; \
    mkdir /opt/ ;\
    mv samtools-${SAMTOOLS_VERSION}.tar.bz2  /opt/ ;\
    cd /opt/ ;\
    tar xjvf samtools-${SAMTOOLS_VERSION}.tar.bz2; \
    cd samtools-${SAMTOOLS_VERSION}/ && make ; \
    cd /opt/ ;\
    rm samtools-${SAMTOOLS_VERSION}.tar.bz2 
    #apk del build-base zlib-dev ca-certificates wget
######安装PYTHON3 PERL HISAT2
#WORKDIR /opt
###RUN apk add bash make wget bzip2 ca-certificates g++\
RUN apk add --no-cache bash make \
    --update perl --no-cache python3 ; \
    cd /opt/ ; \
    wget http://ccb.jhu.edu/software/hisat2/dl/hisat2-2.1.0-source.zip ; \
    unzip hisat2-2.1.0-source.zip ; \
    cd hisat2-2.1.0 && make ; \
    rm /opt/hisat2-2.1.0-source.zip ; \
    if [ -f /usr/bin/python3 ];then ln -s /usr/bin/python3 /usr/bin/python; fi 
##mv samtools-${SAMTOOLS_VERSION}/samtools /opt/; \
##将/bin/sh 改成/bin/bash
RUN if [ -e /bin/sh ];then rm /bin/sh ; fi \
    && if [ -e /bin/bash ];then ln -s /bin/bash /bin/sh ; fi
    
###设置环境变量
ENV PATH /opt:$PATH:/bin:/opt/hisat2-2.1.0
ENV PATH /opt/samtools-${SAMTOOLS_VERSION}/:$PATH