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Dockerfile
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Dockerfile
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#Download base image ubuntu 20.04
#FROM ubuntu:20.04
#FROM rocker/r-ver:3.6.2
FROM rocker/tidyverse:latest
#Now add detailed information about the custom image using the LABEL instruction.
# LABEL about the custom image
LABEL maintainer="[email protected]"
LABEL version="0.1"
LABEL description="This is custom Docker Image for \
the cfmsflow pipeline."
# File Author / Maintainer
MAINTAINER clairemcwhite <[email protected]>
# Prevents interactive tzdata question
ARG DEBIAN_FRONTEND=noninteractive
ENV TZ=America/New_York
# locales \
# vim-tiny \
RUN apt-get update && apt-get install --yes --no-install-recommends \
wget \
git \
# Need one of these three libs for igraph to work
# Do process of elimination
gfortran-7\
libxml2-dev \
libglpk-dev \
python3 \
python3-pip
## Have python command run python3
RUN ln -s /usr/bin/python3 /usr/bin/python && \
ln -s /usr/bin/pip3 /usr/bin/pip
# Install python packages
WORKDIR /usr/src/app
COPY requirements.txt ./
RUN pip install --upgrade pip && \
pip install --no-cache-dir -r requirements.txt
COPY . .
# Install R packages
RUN install2.r --error \
igraph \
dendextend
# Get repositories
RUN git clone --single-branch --branch pandas_update_fix https://github.com/marcottelab/protein_complex_maps.git /indocker_repos/protein_complex_maps
RUN git clone --single-branch --branch master https://github.com/marcottelab/run_TPOT.git /indocker_repos/run_TPOT
# Set environmental variables
ENV PYTHONPATH "${PYTHONPATH}:/indocker_repos/protein_complex_maps"
ENV R_LIBS_SITE "${R_LIBS_SITE}:/usr/local/lib/R/site-library"
ENV LD_LIBRARY_PATH "${LD_LIBRARY_PATH}:/usr/local/lib/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server"