update docker for methylpy dmr build

Dockerfile

@@ -1,12 +1,24 @@
 #############################################################
 # Dockerfile tools for methylpy
 #############################################################
-FROM continuumio/anaconda3
+FROM ubuntu:18.04
+ENV LANG=C.UTF-8 LC_ALL=C.UTF-8
 MAINTAINER Rahul Pisupati <[email protected]>
 LABEL authors="[email protected]" \
     description="Docker image containing all requirements for the nf-core/methylpy pipeline"
-USER root
-RUN apt-get -y -m update && apt-get install -y wget unzip zip libgsl-dev libgsl2 bzip2 build-essential git zlib1g-dev lib32z1-dev
+# Get basic ubuntu packages needed
+ENV PATH /opt/conda/bin:$PATH
+RUN apt-get update --fix-missing && apt-get install -y wget bzip2 ca-certificates \
+    libglib2.0-0 libxext6 libsm6 libxrender1  \
+    git mercurial subversion \
+    build-essential libgsl0-dev
+RUN wget --quiet https://repo.anaconda.com/archive/Anaconda2-5.3.0-Linux-x86_64.sh -O ~/anaconda.sh && \
+    /bin/bash ~/anaconda.sh -b -p /opt/conda && \
+    rm ~/anaconda.sh && \
+    ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh && \
+    echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc && \
+    echo "conda activate base" >> ~/.bashrc
+# RUN apt-get -y -m update && apt-get install -y libgsl-dev libgsl2  build-essential git zlib1g-dev lib32z1-dev
 COPY environment.yml /
 RUN conda env create -f /environment.yml && conda clean -a
 ENV PATH /opt/conda/envs/nfcore-methylseq/bin:$PATH