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updates for Metab4_Docker #1

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dfe6576
Update to xenial, install needed xcms R package and fix war install.
jwhowarth Mar 19, 2018
da6f23c
Add --rm to 'docker run' command so container is auto-removed on exit…
jwhowarth Mar 19, 2018
31e0a8b
Move R package installs into Dockerfile to avoid unnecessary re-insta…
jwhowarth Mar 19, 2018
fdc0310
Merge branch 'master' into master
jsychong Nov 23, 2018
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8 changes: 4 additions & 4 deletions Dockerfile
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Original file line number Diff line number Diff line change
@@ -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"

Expand All @@ -10,13 +10,13 @@ LABEL Description = "MetaboAnalyst 4.0, includes the installation of all necessa
# Thank you to Jack Howarth for his contributions in improving the Dockerfile.

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 && \
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3 changes: 1 addition & 2 deletions metab4script.R
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@@ -1,3 +1,2 @@
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, xcms)
library(Rserve)
Rserve(args=" --no-save --RS-conf /etc/rserve.conf")