From dfe657678fb29456651ddee978126495ab019aca Mon Sep 17 00:00:00 2001 From: jwhowarth Date: Mon, 19 Mar 2018 12:16:22 -0400 Subject: [PATCH 1/3] Update to xenial, install needed xcms R package and fix war install. --- Dockerfile | 14 ++++++-------- 1 file changed, 6 insertions(+), 8 deletions(-) diff --git a/Dockerfile b/Dockerfile index 60ed2d6..f3253cf 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,5 +1,5 @@ -# Use Ubuntu Version 14 -FROM ubuntu:14.04 +# Use Ubuntu Version 16 +FROM ubuntu:16.04 MAINTAINER Xia Lab "jasmine.chong@mail.mcgill.ca" @@ -11,13 +11,13 @@ USER root # graphviz libraries for RGraphviz), then purge apt-get lists RUN apt-get update && \ - apt-get install -y software-properties-common + apt-get install -y software-properties-common sudo RUN apt-get update && \ add-apt-repository ppa:webupd8team/java && \ apt-get update && \ echo oracle-java8-installer shared/accepted-oracle-license-v1-1 select true | /usr/bin/debconf-set-selections && \ - echo "deb http://cran.rstudio.com/bin/linux/ubuntu trusty/" >> /etc/apt/sources.list && \ + echo "deb http://cran.rstudio.com/bin/linux/ubuntu xenial/" >> /etc/apt/sources.list && \ gpg --keyserver keyserver.ubuntu.com --recv-key E084DAB9 && \ gpg -a --export E084DAB9 | sudo apt-key add - && \ apt-get update && \ @@ -45,7 +45,7 @@ RUN apt-get update && \ # Install all R packages from bioconductor -RUN R -e 'source("http://bioconductor.org/biocLite.R"); biocLite(c("Rserve", "RColorBrewer", "xtable", "fitdistrplus","som", "ROCR", "RJSONIO", "gplots", "e1071", "caTools", "igraph", "randomForest", "Cairo", "pls", "pheatmap", "lattice", "rmarkdown", "knitr", "data.table", "pROC", "Rcpp", "caret", "ellipse", "scatterplot3d", "impute", "pcaMethods", "siggenes", "globaltest", "GlobalAncova", "Rgraphviz", "KEGGgraph", "preprocessCore", "genefilter", "SSPA", "sva", "limma", "pacman"))' +RUN R -e 'source("http://bioconductor.org/biocLite.R"); biocLite(c("Rserve", "RColorBrewer", "xtable", "fitdistrplus","som", "ROCR", "RJSONIO", "gplots", "e1071", "caTools", "igraph", "randomForest", "Cairo", "pls", "pheatmap", "lattice", "rmarkdown", "knitr", "data.table", "pROC", "Rcpp", "caret", "ellipse", "scatterplot3d", "impute", "pcaMethods", "siggenes", "globaltest", "GlobalAncova", "Rgraphviz", "KEGGgraph", "preprocessCore", "genefilter", "SSPA", "sva", "limma", "pacman", "xcms"))' ADD rserve.conf /rserve.conf ADD metab4script.R /metab4script.R @@ -76,8 +76,6 @@ ENV METABOANALYST_VERSION 4.09 ENV METABOANALYST_LINK https://www.dropbox.com/s/adkps7jq810dyl4/MetaboAnalyst-4.09.war?dl=0 ENV METABOANALYST_FILE_NAME MetaboAnalyst.war -RUN wget --quiet -O $METABOANALYST_FILE_NAME $METABOANALYST_LINK - -COPY $METABOANALYST_FILE_NAME $DEPLOY_DIR +RUN wget --quiet -O $DEPLOY_DIR/$METABOANALYST_FILE_NAME $METABOANALYST_LINK ENTRYPOINT ["bin/bash"] From da6f23c35da19f677eae15cf5c13fcd3d26d87e6 Mon Sep 17 00:00:00 2001 From: jwhowarth Date: Mon, 19 Mar 2018 12:18:04 -0400 Subject: [PATCH 2/3] Add --rm to 'docker run' command so container is auto-removed on exiting docker. --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 6719c63..177095f 100644 --- a/README.md +++ b/README.md @@ -33,7 +33,7 @@ $ cd ~/Desktop/Metab4_Docker $ docker build -t metab_docker . ### Step 3: Run the Dockerfile, the -ti option will open an interactive Ubuntu terminal into the created container and presents a command prompt -$ docker run -ti --name METAB_DOCKER -p 8080:8080 metab_docker +$ docker run -ti --rm --name METAB_DOCKER -p 8080:8080 metab_docker ## The command prompt will look something like below; you are now in the shell root@760b678fd4bf:/# From 31e0a8b6a115927de9a9a66c29df17a821619ac5 Mon Sep 17 00:00:00 2001 From: jwhowarth Date: Mon, 19 Mar 2018 12:19:23 -0400 Subject: [PATCH 3/3] Move R package installs into Dockerfile to avoid unnecessary re-installs. --- metab4script.R | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/metab4script.R b/metab4script.R index 38d889b..abc3664 100644 --- a/metab4script.R +++ b/metab4script.R @@ -1,4 +1,2 @@ library(Rserve) -library(pacman) -p_load(Rserve, RColorBrewer, xtable, som, fitdistrplus, ROCR, RJSONIO, gplots, e1071, caTools, igraph, randomForest, Cairo, pls, pheatmap, lattice, rmarkdown, knitr, data.table, pROC, Rcpp, caret, ellipse, scatterplot3d, impute, pcaMethods, siggenes, globaltest, GlobalAncova, Rgraphviz, KEGGgraph, preprocessCore, genefilter, SSPA, sva, limma, car) -Rserve(args=" --no-save --RS-conf /etc/rserve.conf") \ No newline at end of file +Rserve(args=" --no-save --RS-conf /etc/rserve.conf")