Dockerfile

FROM rocker/shiny

MAINTAINER Pawel Zayakin "pawel@biomed.lu.lv"

RUN sed -i 's/main$/main contrib non-free/' /etc/apt/sources.list && \
    env DEBIAN_FRONTEND=noninteractive apt-get update && \
    env DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends apt-utils && \
    env DEBIAN_FRONTEND=noninteractive apt-get upgrade -y --no-install-recommends && \
    env DEBIAN_FRONTEND=noninteractive apt-get dist-upgrade -y --no-install-recommends && \
    env DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
        git gawk unzip pigz libjson-perl curl python3-pip libxml2-dev zlib1g-dev libbz2-dev liblzma-dev libssl-dev libproj-dev \
        bowtie bowtie2 cutadapt samtools fastqc ncbi-blast+ ncbi-entrez-direct trnascan-se seqtk radiant \
    && apt-get autoremove -y && apt-get autoclean -y \
    && ln -s /usr/share/perl5/KronaTools/scripts /usr/share/kronatools/scripts
#        r-cran-gdata r-cran-gplots r-cran-ggplot2 r-cran-gridextra r-cran-shinydashboard r-cran-dt r-cran-corrplot \
#        r-cran-shinyjs r-cran-foreach r-cran-domc r-cran-futile.logger r-cran-sendmailr r-cran-openxlsx \
#        r-cran-venndiagram r-bioc-rtracklayer r-cran-xml r-bioc-deseq2 r-bioc-annotate \
#        python3-keras libcurl4-openssl-dev kraken2 rna-star fastp cnvkit picard-tools sortmerna bcftools gffread bedtools python3-htseq
#        libharfbuzz-dev libfribidi-dev libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev libproj-dev

RUN R -e "chooseCRANmirror(graphics =FALSE,ind=1); \
          if (!requireNamespace('BiocManager')) install.packages('BiocManager'); \
          chooseBioCmirror(graphics =FALSE,ind=1); \
          BiocManager::install(c('gdata','gplots','ggplot2','gridExtra','shinydashboard','DT','corrplot','ggalt'), ask=FALSE); \
          BiocManager::install(c('shinyjs','foreach','doMC','futile.logger','sendmailR','openxlsx','seqinr'), ask=FALSE); \
          BiocManager::install(c('EnhancedVolcano','PCAtools','org.Hs.eg.db','edgeR','Rsubread'), ask=FALSE); \
          BiocManager::install(c('VennDiagram','rtracklayer','XML','DESeq2','annotate','GOstats','msa','ape'), ask=FALSE)" # c(,'reticulate')
#    git clone https://github.com/marbl/Krona.git /srv/shiny-server/Krona && cd /srv/shiny-server/Krona/KronaTools && ./install.pl && \
RUN mv /srv/shiny-server /srv/shiny-server.orig && mkdir -p /srv/shiny-server/bin && \
    git clone https://github.com/zajakin/ShortStack.git  /srv/shiny-server/ShortStack && \
    wget http://opengene.org/gencore/gencore -O /srv/shiny-server/bin/gencore && chmod a+x /srv/shiny-server/bin/gencore && \
    wget https://eda.polito.it/isomir-sea/isomiR-SEA_1.6_webpacket.zip -O tmp.zip && \
    unzip -oj tmp.zip isomiR-SEA_1.6_webpacket/isomiR-SEA_OS/Ubuntu_14_04_2LTS_x86_64/isomiR-SEA_1_6 && \
    mv isomiR-SEA_1_6 /srv/shiny-server/bin/isomiR-SEA && rm tmp.zip && \
    pip3 install mieaa keras tensorflow multiqc && git clone https://github.com/tjgu/miTAR.git /srv/shiny-server/miTAR && \
    rm -rf /srv/shiny-server/miTAR/conda  # multiqc && sed -i 's/tf.set_random_seed(sdnum)/tf.random.set_seed(sdnum)/p' /srv/shiny-server/miTAR/predict_multimiRmultimRNA.py
COPY app.R /srv/shiny-server/app.R
COPY LICENSE /srv/shiny-server/LICENSE
COPY README.md /srv/shiny-server/README.md
COPY bin /srv/shiny-server/bin/
COPY shiny /srv/shiny-server/shiny/
COPY gtf_biotypes /srv/shiny-server/gtf_biotypes/
COPY examples /srv/shiny-server/examples/
# git clone https://github.com/zajakin/sRNAflow.git /srv/shiny-server && mkdir -m 777 /home/shiny/R
#chmod 777 . && docker pull ghcr.io/zajakin/srnaflow && docker run -it --rm -p 3838:3838 -v `pwd`:/srv/shiny-server/www -v /tmp/shinylog/:/var/log/shiny-server/ ghcr.io/zajakin/srnaflow
#git clone https://github.com/zajakin/sRNAflow.git && cd sRNAflow && docker build  -t srnaflow . && chmod 777 . && docker run -it --rm -p 3838:3838 -v `pwd`:/srv/shiny-server/www -v /tmp/shinylog/:/var/log/shiny-server/ srnaflow