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snp_call.def
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snp_call.def
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Bootstrap: docker
From: rockylinux:9
# Stage: spython-base
%post
dnf -y update
# Install EPEL repository
dnf install -y epel-release
# Install necessary packages
dnf -y install \
git \
wget \
java-1.8.0-openjdk \
java-1.8.0-openjdk-devel \
autoconf \
automake \
make \
zip \
unzip \
gcc \
perl-Data-Dumper \
zlib-devel \
bzip2 \
bzip2-devel \
xz-devel \
curl-devel \
openssl-devel \
ncurses-devel \
graphviz \
python \
APPS_ROOT=/sing_tools
mkdir -p ${APPS_ROOT}
###############################################
FASTP_VERSION=0.23.4
FASTP_HOME=${APPS_ROOT}/fastp/${FASTP_VERSION}
FASTP_BIN=${FASTP_HOME}/fastp
mkdir -p ${FASTP_HOME}
wget http://opengene.org/fastp/fastp.${FASTP_VERSION} -O ${FASTP_BIN}
chmod a+x ${FASTP_BIN}
###############################################
#BWA = 'bwa/intel/0.7.17'
BWA_VERSION=0.7.17
BWA_HOME=${APPS_ROOT}/bwa/${BWA_VERSION}
PATH=${BWA_HOME}:${PATH}
git clone --branch v${BWA_VERSION} https://github.com/lh3/bwa.git ${BWA_HOME}
cd ${BWA_HOME} && make && cd
###############################################
#PICARD = 'picard/2.17.11'
PICARD_VERSION=2.17.11
JAVA_HOME=/etc/alternatives/jre
PICARD_HOME=${APPS_ROOT}/picard/${PICARD_VERSION}
PICARD_JAR=${PICARD_HOME}/picard-${PICARD_VERSION}.jar
mkdir -p ${PICARD_HOME}
wget https://github.com/broadinstitute/picard/releases/download/${PICARD_VERSION}/picard.jar -O ${PICARD_JAR}
###############################################
#GATK = 'gatk/4.6.1.0'
GATK_VERSION=4.6.1.0
GATK_HOME=${APPS_ROOT}/gatk/${GATK_VERSION}
GATK_LOCAL_JAR=${GATK_HOME}/gatk-package-${GATK_VERSION}-local.jar
GATK_SPARK_JAR=${GATK_HOME}/gatk-package-${GATK_VERSION}-spark.jar
GATK_JAR=${GATK_HOME}/gatk-package-${GATK_VERSION}-local.jar
PATH=${GATK_HOME}:${PATH}
wget https://github.com/broadinstitute/gatk/releases/download/${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
chmod a+x ${GATK_HOME}/gatk
###############################################
#HTSLIB 1.9
HTSLIB_VERSION=1.19.1
HTSLIB_HOME=${APPS_ROOT}/htslib/${HTSLIB_VERSION}
MANPATH=$MANPATH:${HTSLIB_HOME}/share/man
PATH=${PATH}:${HTSLIB_HOME}/bin
LD_LIBRARY_PATH=${HTSLIB_HOME}/lib:${LD_LIBRARY_PATH}
PKG_CONFIG_PATH=${HTSLIB_HOME}/lib/pkgconfig
HTSLIB_HOME=${HTSLIB_HOME}
HTSLIB_INC=${HTSLIB_HOME}/include
HTSLIB_LIB=${HTSLIB_HOME}/lib
wget https://github.com/samtools/htslib/releases/download/${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=${HTSLIB_HOME} \
&& make \
&& make install
###############################################
#bcftools 1.9
BCFTOOLS_VERSION=1.19
BCFTOOLS_HOME=${APPS_ROOT}/bcftools/${BCFTOOLS_VERSION}
wget https://github.com/samtools/bcftools/releases/download/${BCFTOOLS_VERSION}/bcftools-${BCFTOOLS_VERSION}.tar.bz2 \
&& tar xjf bcftools-${BCFTOOLS_VERSION}.tar.bz2 \
&& rm bcftools-${BCFTOOLS_VERSION}.tar.bz2 \
&& cd bcftools-${BCFTOOLS_VERSION} \
&& autoheader \
&& autoconf \
&& ./configure --prefix=${BCFTOOLS_HOME} --with-htslib=${HTSLIB_HOME} \
&& make \
&& make install
###############################################
#SAMTOOLS = 'samtools/intel/1.9'
SAMTOOLS_VERSION=1.19.2
SAMTOOLS_HOME=${APPS_ROOT}/samtools/${SAMTOOLS_VERSION}
MANPATH=${SAMTOOLS_HOME}/share/man
PATH=${SAMTOOLS_HOME}/bin:${PATH}
LD_LIBRARY_PATH=${SAMTOOLS_HOME}/lib:${LD_LIBRARY_PATH}
SAMTOOLS_HOME=${SAMTOOLS_HOME}
SAMTOOLS_INC=${SAMTOOLS_HOME}/include
SAMTOOLS_LIB=${SAMTOOLS_HOME}/lib
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=${HTSLIB_HOME} \
&& make \
&& make install
#################################################
%environment
export APPS_ROOT=/sing_tools
export BWA_VERSION=0.7.17
export BWA_HOME=${APPS_ROOT}/bwa/${BWA_VERSION}
export PATH=${BWA_HOME}:${PATH}
export PICARD_VERSION=2.17.11
export JAVA_HOME=/etc/alternatives/jre
export PICARD_HOME=${APPS_ROOT}/picard/${PICARD_VERSION}
export PICARD_JAR=${PICARD_HOME}/picard-${PICARD_VERSION}.jar
export FASTP_VERSION=0.23.4
export FASTP_HOME=${APPS_ROOT}/fastp/${FASTP_VERSION}
export PATH=${FASTP_HOME}:${PATH}
export GATK_VERSION=4.6.1.0
export GATK_HOME=${APPS_ROOT}/gatk/${GATK_VERSION}
export GATK_LOCAL_JAR=${GATK_HOME}/gatk-package-${GATK_VERSION}-local.jar
export GATK_SPARK_JAR=${GATK_HOME}/gatk-package-${GATK_VERSION}-spark.jar
export GATK_JAR=${GATK_HOME}/gatk-package-${GATK_VERSION}-local.jar
export PATH=${GATK_HOME}:${PATH}
export HTSLIB_VERSION=1.19.1
export HTSLIB_HOME=${APPS_ROOT}/htslib/${HTSLIB_VERSION}
export MANPATH=$MANPATH:${HTSLIB_HOME}/share/man
export PATH=${PATH}:${HTSLIB_HOME}/bin
export LD_LIBRARY_PATH=${HTSLIB_HOME}/lib:${LD_LIBRARY_PATH}
export PKG_CONFIG_PATH=${HTSLIB_HOME}/lib/pkgconfig
export HTSLIB_HOME=${HTSLIB_HOME}
export HTSLIB_INC=${HTSLIB_HOME}/include
export HTSLIB_LIB=${HTSLIB_HOME}/lib
export SAMTOOLS_VERSION=1.19.2
export SAMTOOLS_HOME=${APPS_ROOT}/samtools/${SAMTOOLS_VERSION}
export MANPATH=${SAMTOOLS_HOME}/share/man
export PATH=${SAMTOOLS_HOME}/bin:${PATH}
export LD_LIBRARY_PATH=${SAMTOOLS_HOME}/lib:${LD_LIBRARY_PATH}
export SAMTOOLS_HOME=${SAMTOOLS_HOME}
export SAMTOOLS_INC=${SAMTOOLS_HOME}/include
export SAMTOOLS_LIB=${SAMTOOLS_HOME}/lib
export BCFTOOLS_VERSION=1.19
export BCFTOOLS_HOME=${APPS_ROOT}/bcftools/${BCFTOOLS_VERSION}
export PATH=${BCFTOOLS_HOME}/bin:${PATH}
%runscript
exec /bin/bash "$@"
%startscript
exec /bin/bash "$@"