Dockerfile

FROM centos

MAINTAINER Marie Forest <marie.forest@ladydavis.ca>
MAINTAINER Natacha Beck <natacha.beck@mcgill.ca>

# Install prerequisite
RUN yum update -y

# Install basic packages
RUN yum install -y bzip2 \
                   gcc \
                   git \
                   make \
                   perl \
                   unzip \
                   wget \
                   zlib-devel \
                   which

COPY . imputePrepSanger

WORKDIR /imputePrepSanger/

# INSTALL TOOLS
# 1. Tools that come with this pipeline
RUN chmod 755 /imputePrepSanger/imputePrep_script.sh \ 
    && cp /imputePrepSanger/imputePrep_script.sh /bin/

RUN chmod 755 /imputePrepSanger/HRC-1000G-check-bim_modified.pl \
    && cp /imputePrepSanger/HRC-1000G-check-bim_modified.pl /bin/

RUN chmod 755 /imputePrepSanger/update_build.sh \
    && cp /imputePrepSanger/update_build.sh /bin/ 

RUN chmod 755 /imputePrepSanger/reportRedaction.sh \
    && cp /imputePrepSanger/reportRedaction.sh /bin/


# 2. External tools
# a. bcftools
RUN wget  https://github.com/samtools/bcftools/releases/download/1.3.1/bcftools-1.3.1.tar.bz2 \
 && bunzip2 -f bcftools-1.3.1.tar.bz2 \
 && tar -xvf bcftools-1.3.1.tar \
 && cd bcftools-1.3.1 \
 && make \
 && make install

RUN cp bcftools-1.3.1/bcftools /bin/

# b. plink 
#RUN wget http://pngu.mgh.harvard.edu/~purcell/plink/dist/plink-1.07-x86_64.zip \
#    &&  unzip plink-1.07-x86_64.zip

#RUN cp plink-1.07-x86_64/plink /bin/

RUN unzip plink_linux_x86_64.zip -d ./plink

RUN cp plink/plink /bin/