Dockerfile

FROM centos:7

MAINTAINER "Daniel Vera" vera@genomics.fsu.edu

ENV CGI_BIN=/var/www/cgi-bin
ENV SAMTABIXDIR=/opt/samtabix/
ENV USE_SSL=1
ENV USE_SAMTABIX=1
ENV MACHTYPE=x86_64
ENV PATH=/root/bin/x86_64:/opt/samtabix/:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
ENV JKSRC=jksrc.zip

RUN yum update -y && yum install -y \
 openssl-static.x86_64 \
 usbmuxd-devel.x86_64 \
 mariadb-devel.x86_64 \
 libimobiledevice-devel.x86_64 \
 ghostscript \
 libpng-devel.x86_64 \
 libplist-devel.x86_64 \
 gcc \
 libstdc++-devel.x86_64 \
 libstdc++-static.x86_64 \
 make \
 unzip \
 tcsh \
 perl \
 git \
 rsync \
 wget \
 gcc-c++

RUN mkdir -p /root/bin/x86_64

RUN git clone http://genome-source.cse.ucsc.edu/samtabix.git /opt/samtabix && cd /opt/samtabix && make

RUN cd /opt && curl -sLo jksrc.zip http://hgdownload.cse.ucsc.edu/admin/${JKSRC} && unzip -q jksrc.zip && rm -f jksrc.zip
RUN echo 'L+= -lz' >> /opt/kent/src/inc/common.mk
RUN sed -i 's/hgBeacon//g;s/hgMirror//g' /opt/kent/src/hg/makefile
RUN sed -i 's/#include <uuid\/uuid\.h>//g' /opt/kent/src/inc/uuid.h
RUN cd /opt/kent/src && make clean && make -j $(nproc) utils && make clean