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3.4 years ago
leukippus0116
•
0
Hello, I'm working on NGS data analysis and now I'm trying to build docker image of Variant Calling Pipeline using GATK4(https://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:centos7@sha256:0f4ec88e21daf75124b8a9e5ca03c37a5e937e0e108a255d89049243 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.
