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3 hours ago by

Hello, I'm working on NGS data analysis and now I'm trying to build docker image of Variant Calling Pipeline using GATK4(gencore.bio.nyu.edu/variant-calling-pipeline-gatk4/).

I have encountered an error while building this docker image. I'm new to Bioinformatics so I would appreciate if you could help me solve this problem.

I downloaded docker and cloned successfully as follow;

git clone https://github.com/gencorefacility/variant-calling-pipeline-gatk4.git
cd variant-calling-pipeline-gatk4/

next, I used the following command;

docker build ./ -t cgsbgatk4

Building started and encountered error message as follow;

[+] Building 4.1s (9/19)                                                                                                
 => [internal] load build definition from Dockerfile                                                               0.4s
 => => transferring dockerfile: 84B                                                                                0.0s
 => [internal] load .dockerignore                                                                                  0.5s
 => => transferring context: 2B                                                                                    0.0s
 => [internal] load metadata for docker.io/library/centos:centos7                                                  2.1s
 => [ 1/16] FROM docker.io/library/centos:[email protected]:0f4ec88e21daf75124b8a9e5ca03c37a5e937e0e108a255d89049243  0.0s
 => CACHED [ 2/16] RUN yum install -y epel-release                                                                 0.0s
 => CACHED [ 3/16] RUN yum -y install  git  wget  java-1.8.0-openjdk  java-1.8.0-openjdk-devel  R  autoconf  auto  0.0s
 => CACHED [ 4/16] RUN mkdir -p /apps                                                                              0.0s
 => CACHED [ 5/16] RUN git clone --branch v0.7.17 https://github.com/lh3/bwa.git /apps/bwa/0.7.17                  0.0s
 => ERROR [ 6/16] RUN cd /apps/bwa/0.7.17 && make && cd                                                            1.2s
------                                                                                                                  
 > [ 6/16] RUN cd /apps/bwa/0.7.17 && make && cd:                                                                       
#9 0.686 gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  utils.c -o utils.o              
#9 0.847 gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  kthread.c -o kthread.o          
#9 0.878 gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  kstring.c -o kstring.o          
#9 0.896 gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  ksw.c -o ksw.o                  
#9 0.902 ksw.c:29:23: fatal error: emmintrin.h: No such file or directory
#9 0.902  #include <emmintrin.h>
#9 0.902                        ^
#9 0.902 compilation terminated.
#9 0.918 make: *** [ksw.o] Error 1
------
executor failed running [/bin/sh -c cd ${BWA_HOME} && make && cd]: exit code: 2

Docker file;

FROM centos:centos7

RUN yum install -y epel-release

RUN yum -y install 
    git 
    wget 
    java-1.8.0-openjdk 
    java-1.8.0-openjdk-devel 
    R 
    autoconf 
    automake 
    make 
    gcc 
    perl-Data-Dumper 
    zlib-devel 
    bzip2 
    bzip2-devel 
    xz-devel 
    curl-devel 
    openssl-devel 
    ncurses-devel 
    graphviz


ENV APPS_ROOT /apps
RUN mkdir -p ${APPS_ROOT}

###############################################
#BWA = 'bwa/intel/0.7.17'

ENV BWA_VERSION 0.7.17

ENV BWA_HOME ${APPS_ROOT}/bwa/${BWA_VERSION}
ENV PATH ${BWA_HOME}:${PATH}

RUN git clone --branch v${BWA_VERSION} https://github.com/lh3/bwa.git ${BWA_HOME}
RUN cd ${BWA_HOME} && make && cd

###############################################
#PICARD = 'picard/2.17.11'

ENV PICARD_VERSION 2.17.11

ENV JAVA_HOME /etc/alternatives/jre
ENV PICARD_HOME ${APPS_ROOT}/picard/${PICARD_VERSION}
ENV PICARD_JAR ${PICARD_HOME}/picard-${PICARD_VERSION}.jar

RUN mkdir -p ${PICARD_HOME}
RUN wget https://github.com/broadinstitute/picard/releases/download/${PICARD_VERSION}/picard.jar -O ${PICARD_JAR}

###############################################
#GATK = 'gatk/4.1.3.0'

ENV GATK_VERSION 4.1.3.0

ENV GATK_HOME ${APPS_ROOT}/gatk/${GATK_VERSION}

ENV GATK_LOCAL_JAR ${GATK_HOME}/gatk-package-${GATK_VERSION}-local.jar
ENV GATK_SPARK_JAR ${GATK_HOME}/gatk-package-${GATK_VERSION}-spark.jar
ENV GATK_JAR ${GATK_HOME}/gatk-package-${GATK_VERSION}-local.jar
ENV PATH ${GATK_HOME}:${PATH}

RUN wget https://github.com/broadinstitute/gatk/releases/download/${GATK_VERSION}/gatk-${GATK_VERSION}.zip 
        && mkdir ${APPS_ROOT}/gatk 
        && unzip gatk-${GATK_VERSION}.zip 
        && mv gatk-${GATK_VERSION} ${APPS_ROOT}/gatk/${GATK_VERSION} 
        && rm gatk-${GATK_VERSION}.zip

###############################################
#R = 'r/intel/3.4.2'
# INSTALLED MOST CURRENT R

###############################################
#HTSLIB 1.9
ENV HTSLIB_VERSION 1.9
ENV HTSLIB_HOME ${APPS_ROOT}/htslib/${HTSLIB_VERSION}

ENV MANPATH $MANPATH:${HTSLIB_HOME}/share/man
ENV PATH ${PATH}:${HTSLIB_HOME}/bin
ENV LD_LIBRARY_PATH ${HTSLIB_HOME}/lib:${LD_LIBRARY_PATH}
ENV PKG_CONFIG_PATH ${HTSLIB_HOME}/lib/pkgconfig
ENV HTSLIB_HOME ${HTSLIB_HOME}
ENV HTSLIB_INC ${HTSLIB_HOME}/include
ENV HTSLIB_LIB ${HTSLIB_HOME}/lib

RUN wget https://github.com/samtools/htslib/releases/download/${HTSLIB_VERSION}/htslib-${HTSLIB_VERSION}.tar.bz2 
    && tar xjf htslib-${HTSLIB_VERSION}.tar.bz2 
    && rm htslib-${HTSLIB_VERSION}.tar.bz2 
    && cd htslib-${HTSLIB_VERSION} 
    && autoheader 
    && autoconf  
    && ./configure --prefix=${HTSLIB_HOME} 
    && make 
    && make install

###############################################
#SAMTOOLS = 'samtools/intel/1.9'

ENV SAMTOOLS_VERSION 1.9
ENV SAMTOOLS_HOME ${APPS_ROOT}/samtools/${SAMTOOLS_VERSION}

ENV MANPATH ${SAMTOOLS_HOME}/share/man
ENV PATH ${SAMTOOLS_HOME}/bin:${PATH}
ENV LD_LIBRARY_PATH ${SAMTOOLS_HOME}/lib:${LD_LIBRARY_PATH}
ENV SAMTOOLS_HOME ${SAMTOOLS_HOME}
ENV SAMTOOLS_INC ${SAMTOOLS_HOME}/include
ENV SAMTOOLS_LIB ${SAMTOOLS_HOME}/lib

RUN wget https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VERSION}/samtools-${SAMTOOLS_VERSION}.tar.bz2 
    && tar xjf samtools-${SAMTOOLS_VERSION}.tar.bz2 
    && rm samtools-${SAMTOOLS_VERSION}.tar.bz2 
    && cd samtools-${SAMTOOLS_VERSION} 
    && autoheader 
    && autoconf -Wno-syntax 
    && ./configure --prefix=${SAMTOOLS_HOME} --with-htslib=${HTSLIB_HOME} 
    && make 
    && make install

###############################################
#SNPEFF = 'snpeff/4.3'

ENV SNPEFF_VERSION 4_3i
ENV SNPEFF_HOME ${APPS_ROOT}/snpeff/${SNPEFF_VERSION}

ENV SNPEFF_JAR ${SNPEFF_HOME}/snpEff.jar
ENV SNPSIFT_JAR ${SNPEFF_HOME}/SnpSift.jar

RUN wget -O snpEff_v${SNPEFF_VERSION}_core.zip  https://sourceforge.net/projects/snpeff/files/snpEff_v${SNPEFF_VERSION}_core.zip/download# 
        && mkdir ${APPS_ROOT}/snpeff 
        && unzip snpEff_v${SNPEFF_VERSION}_core.zip 
        && mv snpEff ${APPS_ROOT}/snpeff/${SNPEFF_VERSION}

###############################################
# R Packages Installation
RUN R -e "install.packages('ggplot2', repos = 'http://cran.us.r-project.org')"
RUN R -e "install.packages('gsalib', repos = 'http://cran.us.r-project.org')"
RUN R -e "install.packages('reshape', repos = 'http://cran.us.r-project.org')"
RUN R -e "install.packages('gplots', repos = 'http://cran.us.r-project.org')"

Can somebody help me understand this problem? Thank you.



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