scRNA.seq.course
/
Dockerfile

FROM quay.io/cellgeni/cellgeni-jupyter:14.05-01

USER root

# pre-requisites
RUN apt-get update && apt-get install -yq --no-install-recommends \
    libncurses5-dev \
    libncursesw5-dev \
    procps \
    texlive

# Install FastQC
RUN curl -fsSL http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.5.zip -o /opt/fastqc_v0.11.5.zip && \
    unzip /opt/fastqc_v0.11.5.zip -d /opt/ && \
    chmod 755 /opt/FastQC/fastqc && \
    ln -s /opt/FastQC/fastqc /usr/local/bin/fastqc && \
    rm /opt/fastqc_v0.11.5.zip

# Install Kallisto
RUN curl -fsSL https://github.com/pachterlab/kallisto/releases/download/v0.43.1/kallisto_linux-v0.43.1.tar.gz -o /opt/kallisto_linux-v0.43.1.tar.gz && \
    tar xvzf /opt/kallisto_linux-v0.43.1.tar.gz -C /opt/ && \
    ln -s /opt/kallisto_linux-v0.43.1/kallisto /usr/local/bin/kallisto && \
    rm /opt/kallisto_linux-v0.43.1.tar.gz

# Install STAR
RUN git clone https://github.com/alexdobin/STAR.git /opt/STAR && \
    ln -s /opt/STAR/bin/Linux_x86_64/STAR /usr/local/bin/STAR && \
    ln -s /opt/STAR/bin/Linux_x86_64/STARlong /usr/local/bin/STARlong

# Install SAMTools
RUN curl -fsSL https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2 -o /opt/samtools-1.9.tar.bz2 && \
    tar xvjf /opt/samtools-1.9.tar.bz2 -C /opt/ && \
    cd /opt/samtools-1.9 && \
    make && \
    make install && \
    rm /opt/samtools-1.9.tar.bz2

# Install featureCounts
RUN curl -fsSL http://downloads.sourceforge.net/project/subread/subread-1.5.1/subread-1.5.1-Linux-x86_64.tar.gz -o /opt/subread-1.5.1-Linux-x86_64.tar.gz && \
    tar xvf /opt/subread-1.5.1-Linux-x86_64.tar.gz -C /opt/ && \
    ln -s /opt/subread-1.5.1-Linux-x86_64/bin/featureCounts /usr/local/bin/featureCounts && \
    rm /opt/subread-1.5.1-Linux-x86_64.tar.gz

# Install cutadapt and MAGIC and awscli (to download data)
RUN pip install cutadapt magic-impute awscli

# Install TrimGalore
RUN mkdir /opt/TrimGalore && \
    curl -fsSL https://github.com/FelixKrueger/TrimGalore/archive/0.4.5.zip -o /opt/TrimGalore/trim_galore_v0.4.5.zip && \
    unzip /opt/TrimGalore/trim_galore_v0.4.5.zip -d /opt/TrimGalore && \
    ln -s /opt/TrimGalore/trim_galore /usr/local/bin/trim_galore && \
    rm /opt/TrimGalore/trim_galore_v0.4.5.zip

# Install bedtools2
RUN curl -fsSL https://github.com/arq5x/bedtools2/releases/download/v2.27.1/bedtools-2.27.1.tar.gz -o /opt/bedtools-2.27.1.tar.gz && \
    tar xvzf /opt/bedtools-2.27.1.tar.gz -C /opt/ && \
    cd /opt/bedtools2 && \
    make && \
    cd - && \
    cp /opt/bedtools2/bin/* /usr/local/bin && \
    rm /opt/bedtools-2.27.1.tar.gz

# install CRAN packages
RUN apt-get update && apt-get install -yq --no-install-recommends \
    r-cran-devtools \
    r-cran-tidyverse \
    r-cran-pheatmap \
    r-cran-plyr \
    r-cran-dplyr \
    r-cran-readr \
    r-cran-reshape \
    r-cran-reshape2 \
    r-cran-reticulate \
    r-cran-viridis \
    r-cran-ggplot2 \
    r-cran-ggthemes \
    r-cran-cowplot \
    r-cran-ggforce \
    r-cran-ggridges \
    r-cran-ggrepel \
    r-cran-gplots \
    r-cran-igraph \
    r-cran-car \
    r-cran-ggpubr \
    r-cran-httpuv \
    r-cran-xtable \
    r-cran-sourcetools \
    r-cran-modeltools \
    r-cran-R.oo \
    r-cran-R.methodsS3 \
    r-cran-shiny \
    r-cran-later \
    r-cran-checkmate \
    r-cran-bibtex \
    r-cran-lsei \
    r-cran-bit \
    r-cran-segmented \
    r-cran-mclust \
    r-cran-flexmix \
    r-cran-prabclus \
    r-cran-diptest \
    r-cran-mvtnorm \
    r-cran-robustbase \
    r-cran-kernlab \
    r-cran-trimcluster \
    r-cran-proxy \
    r-cran-R.utils \
    r-cran-htmlwidgets \
    r-cran-hexbin \
    r-cran-crosstalk \
    r-cran-promises \
    r-cran-acepack \
    r-cran-zoo \
    r-cran-npsurv \
    r-cran-iterators \
    r-cran-snow \
    r-cran-bit64 \
    r-cran-permute \
    r-cran-mixtools \
    r-cran-lars \
    r-cran-ica \
    r-cran-fpc \
    r-cran-ape \
    r-cran-pbapply \
    r-cran-irlba \
    r-cran-dtw \
    r-cran-plotly \
    r-cran-metap \
    r-cran-lmtest \
    r-cran-fitdistrplus \
    r-cran-png \
    r-cran-foreach \
    r-cran-vegan \
    r-cran-tidyr \
    r-cran-withr \
    r-cran-magrittr \
    r-cran-rmpi \
    r-cran-biocmanager \
    r-cran-knitr \
    r-cran-statmod \
    r-cran-mvoutlier \
    r-cran-penalized \
    r-cran-mgcv \
    r-cran-corrplot

# Install other CRAN
RUN Rscript -e 'install.packages(c("Seurat", "rJava", "umap", "bookdown", "cluster", "KernSmooth", "ROCR", "googleVis", "ggbeeswarm", "SLICER", "ggfortify", "mclust", "Rmagic", "DrImpute"))'

# Install Bioconductor packages
RUN Rscript -e 'BiocManager::install(c("graph", "RBGL", "gtools", "xtable", "pcaMethods", "limma", "SingleCellExperiment", "Rhdf5lib", "scater", "scran", "RUVSeq", "sva", "SC3", "TSCAN", "monocle", "destiny", "DESeq2", "edgeR", "MAST", "scmap", "biomaRt", "MultiAssayExperiment", "SummarizedExperiment"))'

# install github packages
RUN Rscript -e 'devtools::install_github(c("immunogenomics/harmony", "LTLA/beachmat", "MarioniLab/DropletUtils", "tallulandrews/M3Drop", "hemberg-lab/scRNA.seq.funcs", "Vivianstats/scImpute", "theislab/kBET", "kieranrcampbell/ouija", "hemberg-lab/scfind"))'

# download data and extra files from S3
COPY ./poststart.sh /home/jovyan

# add course files
COPY course_files /home/jovyan
RUN chmod -R 777 /home/jovyan

USER $NB_UID