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Dockerfile
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FROM bioconductor/bioconductor_docker:latest
WORKDIR /home/rstudio
COPY --chown=rstudio:rstudio . /home/rstudio/
RUN apt-get update && \
apt-get install -y --no-install-recommends \
apt-utils \
libglpk-dev \
libcurl4-openssl-dev \
libxml2-dev \
libssl-dev && \
apt-get clean && \
rm -rf /var/lib/apt/lists/*
# ANNOVAR
ENV TOOLS=/home/TOOLS/tools
ENV TOOL_NAME=annovar
ENV TOOL_VERSION=current
ENV TARBALL_LOCATION=http://www.openbioinformatics.org/annovar/download/0wgxR2rIVP/
ENV TARBALL=annovar.latest.tar.gz
ENV TARBALL_FOLDER=$TOOL_NAME
ENV DEST=$TOOLS/$TOOL_NAME/$TOOL_VERSION
ENV PATH=$TOOLS/$TOOL_NAME/$TOOL_VERSION/bin:$PATH
# http://www.openbioinformatics.org/annovar/download/0wgxR2rIVP/annovar.latest.tar.gz
# INSTALL
RUN wget $TARBALL_LOCATION/$TARBALL ; \
tar xf $TARBALL --wildcards *pl ; \
rm -rf $TARBALL ; \
cd $TARBALL_FOLDER ; \
mkdir -p $TOOLS/$TOOL_NAME/$TOOL_VERSION/bin ; \
cp *pl $TOOLS/$TOOL_NAME/$TOOL_VERSION/bin/ -R ; \
mkdir /databases ; \
ln -s /databases/ $TOOLS/$TOOL_NAME/$TOOL_VERSION/bin/humandb ; \
cd ../ ; \
rm -rf $TARBALL_FOLDER ;
ENV SAMTOOLS_VERSION 1.9
ENV HTSLIB_VERSION 1.9
RUN cd /; \
wget -q https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VERSION}/samtools-${SAMTOOLS_VERSION}.tar.bz2; \
tar xjf samtools-${SAMTOOLS_VERSION}.tar.bz2; \
cd /samtools-${SAMTOOLS_VERSION}/ && ./configure && make; \
mv /samtools-${SAMTOOLS_VERSION}/samtools /bin/; \
cd htslib-${HTSLIB_VERSION}/ && ./configure && make; \
mv htsfile libhts.so* tabix bgzip /bin; \
rm -rf /samtools*;
# BCFTOOLS
ENV TOOLS=/home/TOOLS/tools
ENV TOOL_NAME=bcftools
ENV TOOL_VERSION=1.9
ENV DEST=$TOOLS/$TOOL_NAME/$TOOL_VERSION
ENV PATH=$TOOLS/$TOOL_NAME/$TOOL_VERSION/bin:$PATH
WORKDIR /tmp
RUN wget https://github.com/samtools/bcftools/releases/download/$TOOL_VERSION/bcftools-$TOOL_VERSION.tar.bz2 && \
tar --bzip2 -xf bcftools-$TOOL_VERSION.tar.bz2
WORKDIR /tmp/bcftools-$TOOL_VERSION
RUN make prefix=$DEST && \
make prefix=$DEST install
WORKDIR /
RUN ln -s $DEST/bin/bcftools /usr/bin/bcftools && \
rm -rf /tmp/bcftools-$TOOL_VERSION
# VCFTOOLS
ENV ZIP=vcftools-0.1.15.tar.gz
ENV URL=https://github.com/vcftools/vcftools/releases/download/v0.1.15/
ENV FOLDER=vcftools-0.1.15
ENV DST=/tmp
ENV PATH=$FOLDER/bin:$PATH
RUN wget $URL/$ZIP -O $DST/$ZIP && \
tar xvf $DST/$ZIP -C $DST && \
rm $DST/$ZIP && \
cd $DST/$FOLDER && \
./configure && \
make && \
make install && \
cd / && \
rm -rf $DST/$FOLDER
ENV PATH=$FOLDER/bin:$PATH
RUN Rscript -e \
'options(repos=c(CRAN="https://cran.r-project.org", BiocManager::repositories())); \
install.packages("rmarkdown"); \
install.packages("dplyr"); \
install.packages("ggplot2"); \
install.packages("data.table"); \
install.packages("reshape2"); \
install.packages("latex2exp"); \
install.packages("BiocManager"); \
BiocManager::install(); \
BiocManager::install("GenomicFeatures"); \
BiocManager::install("GenomicRanges", ask=FALSE); \
BiocManager::install("SeqArray", ask=FALSE); \
BiocManager::install("SNPRelate", ask=FALSE); \
BiocManager::install("GENESIS", ask=FALSE); \
BiocManager::install("TxDb.Hsapiens.UCSC.hg19.knownGene", ask=FALSE); \
BiocManager::install("GMMAT", ask=FALSE); \
BiocManager::install("EBImage", ask=FALSE);'