Mercurial > repos > dlalgroup > pmids_to_pubtator_matrix
diff Dockerfile @ 0:3f4adc85ba5d draft
"planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
| author | dlalgroup |
|---|---|
| date | Thu, 24 Sep 2020 02:01:50 +0000 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Dockerfile Thu Sep 24 02:01:50 2020 +0000 @@ -0,0 +1,38 @@ +FROM rocker/r-ubuntu:20.04 +WORKDIR /simtext +COPY . . + +RUN apt-get update -qq && apt-get -y upgrade && apt-get -y --no-install-recommends install \ + libssl-dev \ + file \ + zlib1g-dev \ + libcurl4-openssl-dev \ + libxml2-dev \ + libjpeg-dev \ + && Rscript -e 'if (!require("shiny")) install.packages("shiny", repos="https://cloud.r-project.org");' \ + && Rscript -e 'if (!require("plotly")) install.packages("plotly", repos="https://cloud.r-project.org");' \ + && Rscript -e 'if (!require("DT")) install.packages("DT", repos="https://cloud.r-project.org");' \ + && Rscript -e 'if (!require("shinycssloaders")) install.packages("shinycssloaders", repos="https://cloud.r-project.org");' \ + && Rscript -e 'if (!require("shinythemes")) install.packages("shinythemes", repos="https://cloud.r-project.org");' \ + && Rscript -e 'if (!require("tableHTML")) install.packages("tableHTML", repos="https://cloud.r-project.org");' \ + && Rscript -e 'if (!require("argparse")) install.packages("argparse", repos="https://cloud.r-project.org");' \ + && Rscript -e 'if (!require("PubMedWordcloud")) install.packages("PubMedWordcloud", repos="https://cloud.r-project.org");' \ + && Rscript -e 'if (!require("ggplot2")) install.packages("ggplot2", repos="https://cloud.r-project.org");' \ + && Rscript -e 'if (!require("stringr")) install.packages("stringr", repos="https://cloud.r-project.org");' \ + && Rscript -e 'if (!require("tidyr")) install.packages("tidyr", repos="https://cloud.r-project.org");' \ + && Rscript -e 'if (!require("magrittr")) install.packages("magrittr", repos="https://cloud.r-project.org");' \ + && Rscript -e 'if (!require("plyr")) install.packages("plyr", repos="https://cloud.r-project.org");' \ + && Rscript -e 'if (!require("ggpubr")) install.packages("ggpubr", repos="https://cloud.r-project.org");' \ + && Rscript -e 'if (!require("rafalib")) install.packages("rafalib", repos="https://cloud.r-project.org");' \ + && Rscript -e 'if (!require("RColorBrewer")) install.packages("RColorBrewer", repos="https://cloud.r-project.org");' \ + && Rscript -e 'if (!require("dendextend")) install.packages("dendextend", repos="https://cloud.r-project.org");' \ + && Rscript -e 'if (!require("Rtsne")) install.packages("Rtsne", repos="https://cloud.r-project.org");' \ + && Rscript -e 'if (!require("umap")) install.packages("umap", repos="https://cloud.r-project.org");' \ + && Rscript -e 'if (!require("reutils")) install.packages("reutils", repos="https://cloud.r-project.org");' \ + && Rscript -e 'if (!require("textclean")) install.packages("textclean", repos="https://cloud.r-project.org");' \ + && Rscript -e 'if (!require("easyPubMed")) install.packages("easyPubMed", repos="https://cloud.r-project.org");' \ + && Rscript -e 'if (!require("RCurl")) install.packages("RCurl", repos="https://cloud.r-project.org");' \ + && Rscript -e 'if (!require("SnowballC")) install.packages("SnowballC", repos="https://cloud.r-project.org");' \ + && Rscript -e 'if (!require("SemNetCleaner")) install.packages("SemNetCleaner", repos="https://cloud.r-project.org");' + +ENV PATH "/simtext/:${PATH}"