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Dockerfile
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FROM jupyter/datascience-notebook:lab-3.0.14
#RaceID
RUN R -e 'install.packages("RaceID",dep=TRUE,repos="https://cran.rstudio.com/"); if (!library(RaceID, logical.return=T)) quit(status=10)'
##ssam
RUN R -e 'install.packages("sctransform",dep=TRUE,repos="https://cran.rstudio.com/"); if (!library(sctransform, logical.return=T)) quit(status=10)'
RUN R -e 'install.packages("feather",dep=TRUE,repos="https://cran.rstudio.com/"); if (!library(feather, logical.return=T)) quit(status=10)'
RUN pip install --no-cache-dir --upgrade pip && \
pip install --no-cache-dir pyarrow && \
pip install --no-cache-dir ssam
#R biocpackage and dependcy
RUN R -e 'install.packages("shinythemes",dep=TRUE,repos="https://cran.rstudio.com/"); if (!library(shinythemes, logical.return=T)) quit(status=10)'
RUN R -e 'install.packages("shinyBS",dep=TRUE,repos="https://cran.rstudio.com/"); if (!library(shinyBS, logical.return=T)) quit(status=10)'
RUN R -e 'install.packages("cowplot",dep=TRUE,repos="https://cran.rstudio.com/"); if (!library(cowplot, logical.return=T)) quit(status=10)'
RUN R -e 'install.packages("BiocManager",dep=TRUE,repos="https://cran.rstudio.com/"); if (!library(BiocManager, logical.return=T)) quit(status=10)'
RUN R -e 'install.packages("stringdist",dep=TRUE,repos="https://cran.rstudio.com/"); if (!library(stringdist, logical.return=T)) quit(status=10)'
#RUN R bioc_pcks <- c("GenomicRanges","GenomicFeatures","GenomicAlignments","AnnotationDbi","Rsubread")
RUN R -e 'BiocManager::install("BiocDockerManager")'
##bwa
RUN conda install -c bioconda bwa
#kallisto
RUN conda install -c bioconda kallisto
#old bustools
#RUN conda install -c bioconda bustools
##install cmake
USER root
RUN apt-get update \
&& apt-get install --assume-yes --no-install-recommends --quiet \
ca-certificates \
cmake \
git \
g++ \
make \
libzip-dev \
&& apt-get clean all
USER ${user}
WORKDIR $HOME
## bustools_dev
RUN git clone https://github.com/Yenaled/bustools.git && \
mkdir -p $HOME/bustools/build && \
cd $HOME/bustools/build \
&& cmake .. \
&& make \
&& make install
#RUN cd src
#RUN mv bustools bustools_dev
#RUN ENV PATH=$HOME/bustools/build/src/:${PATH}
#Samtools
USER root
RUN apt-get update && apt-get install --no-install-recommends -y \
libncurses5-dev \
libbz2-dev \
liblzma-dev \
libcurl4-gnutls-dev \
zlib1g-dev \
libssl-dev \
gnuplot \
ca-certificates && \
apt-get autoclean && rm -rf /var/lib/apt/lists/*
USER ${user}
WORKDIR $HOME
ARG SAMTOOLSVER=1.13
RUN wget https://github.com/samtools/samtools/releases/download/${SAMTOOLSVER}/samtools-${SAMTOOLSVER}.tar.bz2
RUN tar -xjf samtools-${SAMTOOLSVER}.tar.bz2
RUN rm samtools-${SAMTOOLSVER}.tar.bz2 && \
cd samtools-${SAMTOOLSVER} && \
./configure --prefix $(pwd) && \
make
ENV PATH=$HOME/samtools-${SAMTOOLSVER}:${PATH}
#update conda
RUN conda update -n base conda
RUN conda install -c anaconda networkx>=2.5
#install new version of RACEID
WORKDIR newRaceID
COPY RaceID newRaceID/RaceID
RUN R -e 'install.packages("runner",dep=TRUE,repos="https://cran.rstudio.com/");'
RUN R -e 'install.packages("harmony",dep=TRUE,repos="https://cran.rstudio.com/");'
RUN R -e 'install.packages("leiden",dep=TRUE,repos="https://cran.rstudio.com/");'
RUN R -e 'install.packages("newRaceID/RaceID",dep=TRUE,repos=NULL,type="source");'
WORKDIR $HOME
#zUMI
WORKDIR $HOME
#RUN git clone https://github.com/sdparekh/zUMIs.git
#ENV PATH=$HOME
#cellranger
#WORKDIR $HOME
#ENV CELLRANGER_VER 6.0.2
#COPY cellranger-$CELLRANGER_VER.tar.gz cellranger-$CELLRANGER_VER.tar.gz
#RUN tar -xzvf cellranger-$CELLRANGER_VER.tar.gz && \
# #echo $(ls)
# #alias cellranger=$HOME/cellranger-$CELLRANGER_VER/cellranger
# echo "#!/bin/bash\n$HOME/cellranger-$CELLRANGER_VER/cellranger" > /opt/conda/bin/cellranger && \
# chmod +x /opt/conda/bin/cellranger
#ENV PATH=${PATH}:$HOME/cellranger-$CELLRANGER_VER