pantelispanka/biocpu repository overview

biocpu image let's you have bioconductor and OpenCPU on the same image.

This way you can create rest API's on bioconductor packages.

Example usage:

from pantelispanka/biocpu:latest

RUN R -e "install.packages(c('jsonlite', 'RCurl','Matrix', 'vegan'), repos='http://cran.cc.uoc.gr/mirrors/CRAN/')"

RUN Rscript -e 'source("http://bioconductor.org/biocLite.R")' -e 'biocLite(c("org.Hs.eg.db", "GSEABase", "GOstats", "Category", "GO.db"))'

COPY yourPackage.tar.gz /packages/

COPY server.conf /etc/opencpu/

USER root

RUN R CMD INSTALL /packages/yourPackage.tar.gz --library=/usr/local/lib/R/site-library

CMD /usr/sbin/apache2ctl -D FOREGROUND

explanation:

RUN R -e "install.packages(c('jsonlite', 'RCurl','Matrix', 'vegan'), repos='http://cran.cc.uoc.gr/mirrors/CRAN/⁠')"

installs your package dependencies

RUN Rscript -e 'source("http://bioconductor.org/biocLite.R⁠")' -e 'biocLite(c("org.Hs.eg.db", "GSEABase", "GOstats", "blockcluster", "Category", "GO.db"))'

installs your bioconductor dependencies

COPY server.conf /etc/opencpu/

Replaces the server.conf for the OpenCPU server. This may be useful since bioconductor may need more time than the default time of OpenCPU

Install your application and run the image

USER root

RUN R CMD INSTALL /packages/yourPackage.tar.gz --library=/usr/local/lib/R/site-library

CMD /usr/sbin/apache2ctl -D FOREGROUND