diff GalFilter/Dockerfile @ 3:cfd7c4aa5c26 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GalFilter/Dockerfile	Fri Jan 03 04:09:28 2020 -0500
@@ -0,0 +1,87 @@
+################################################################################
+### 
+### [CONTAINER CORE FUNCTIONS]: 
+###     install "Tool - Generic Filter" Galaxy tool (and required third part softwares, libraries, ...).
+### [NOTE]
+###     please refer to README.md and about_docker.md files for further informations
+### 
+################################################################################
+
+################################################################################
+### fix parent containter
+FROM ubuntu:16.04
+
+################################################################################
+### set author
+MAINTAINER Nils Paulhe <[e-mail]>
+
+################################################################################
+### sets the environment variables
+ENV TOOL_VERSION = "release_2016.03.03"
+ENV CONTAINER_VERSION = 0.1
+
+LABEL version = "${CONTAINER_VERSION}"
+LABEL tool_version = "${TOOL_VERSION}"
+
+################################################################################
+### install third part tools 
+
+# add debian repo for latest version of R
+RUN echo "deb http://cran.univ-paris1.fr/bin/linux/ubuntu trusty/" >> /etc/apt/sources.list && \
+    apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9 
+
+# Update and upgrade system
+RUN apt-get update && \
+    apt-get -y upgrade
+
+# install R
+RUN apt-get install -y \ 
+    r-base \
+    libcurl4-openssl-dev \
+    libxml2-dev
+# NOTE: add `apt-get install -y git` if required
+
+# init R env. (Docker)
+RUN echo "r <- getOption('repos'); r['CRAN'] <- 'http://cran.us.r-project.org'; options(repos = r);" > ~/.Rprofile
+
+# install R libs
+RUN Rscript -e "install.packages('batch', dep=TRUE)"
+
+################################################################################
+### install core scripts
+
+# init. WORKDIR
+RUN [ "mkdir", "/scripts" ]
+
+#
+# [NOTE] to add scripts, we have two options: get them from GitHub OR copy them from this directory
+# 
+
+# get scripts using Git (option 1)
+# RUN cd /scripts && \
+#    git clone -b release/${TOOL_VERSION} --recursive https://github.com/workflow4metabolomics/tool-generic_filter.git
+
+# copy scripts files from this directory (option 2)
+COPY "." "/scripts/"
+
+## set WORKDIR
+# WORKDIR "/scripts"
+
+# set authorizations
+RUN ["chmod", "a+x", "/scripts/filter_wrap.R"]
+
+# make tool accessible through PATH
+ENV PATH = $PATH:/scripts
+
+################################################################################
+### clean
+RUN apt-get clean && \
+    apt-get autoremove -y && \
+    rm -rf /var/lib/{apt,dpkg,cache,log}/ /tmp/* /var/tmp/*
+# NOTE: run `apt-get remove -y git && \` if required
+
+################################################################################
+### Define Entry point script
+## ENTRYPOINT ["/scripts/filter_wrap.R"]
+
+### [END]
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