From 27ef7f166598c1ed977b42a957306aabc85d10da Mon Sep 17 00:00:00 2001
From: biolxy <biolxy@aliyun.com>
Date: Thu, 21 Nov 2019 15:44:08 +0800
Subject: [PATCH] 1, Modify python in the container to be python3;2, change
 'FROM' to 'FROM ubuntu:16.04';3 ,Specifies module version information for PIP
 installation;

---
 Dockerfile | 78 ++++++++++++++++++++++++++++++++++++------------------
 1 file changed, 52 insertions(+), 26 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 226fcae..5a77a0b 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -15,50 +15,65 @@
 #################################################################
 
 # Source Image
-FROM biocontainers/biocontainers:latest
+FROM ubuntu:16.04
 
 ################## BEGIN INSTALLATION ###########################
 USER root
 
 # install
+RUN printf "deb http://dk.archive.ubuntu.com/ubuntu/ xenial main\ndeb http://dk.archive.ubuntu.com/ubuntu/ xenial universe\n" >> /etc/apt/sources.list
 RUN apt-get update && apt-get install -y software-properties-common \
-&& apt-get update && apt-get install -y \
     gcc-4.9 \
     g++-4.9 \
     coinor-cbc \
     zlib1g-dev \
     libbz2-dev \
+    libfreetype6-dev \
+    libxft-dev \
+    curl \
+    git \
+    cmake \
 && update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-4.9 60 --slave /usr/bin/g++ g++ /usr/bin/g++-4.9 \
 && rm -rf /var/lib/apt/lists/* \
-&& apt-get clean \
-&& apt-get purge
+&& apt-get clean && apt-get purge
 
 #HLA Typing
 #OptiType dependecies
-RUN curl -O https://support.hdfgroup.org/ftp/HDF5/current18/bin/hdf5-1.8.21-Std-centos7-x86_64-shared_64.tar.gz \
-    && tar -xvf hdf5-1.8.21-Std-centos7-x86_64-shared_64.tar.gz \
-    && mv hdf5-1.8.21-Std-centos7-x86_64-shared_64/bin/* /usr/local/bin/ \
-    && mv hdf5-1.8.21-Std-centos7-x86_64-shared_64/lib/* /usr/local/lib/ \
-    && mv hdf5-1.8.21-Std-centos7-x86_64-shared_64/include/* /usr/local/include/ \
-    && mv hdf5-1.8.21-Std-centos7-x86_64-shared_64/share/* /usr/local/share/ \
-    && rm -rf hdf5-1.8.21-Std-centos7-x86_64-shared_64/ \
+WORKDIR /
+# COPY hdf5-1.8.21-Std-centos7-x86_64-shared_64.tar.gz .
+RUN curl -O https://support.hdfgroup.org/ftp/HDF5/current18/bin/hdf5-1.8.21-Std-centos7-x86_64-shared_64.tar.gz && \
+    tar -xvf hdf5-1.8.21-Std-centos7-x86_64-shared_64.tar.gz \
+    && mv hdf5/bin/* /usr/local/bin/ \
+    && mv hdf5/lib/* /usr/local/lib/ \
+    && mv hdf5/include/* /usr/local/include/ \
+    && mv hdf5/share/* /usr/local/share/ \
+    && rm -rf hdf5/ \
     && rm -f hdf5-1.8.21-Std-centos7-x86_64-shared_64.tar.gz
 
 ENV LD_LIBRARY_PATH /usr/local/lib:$LD_LIBRARY_PATH
 ENV HDF5_DIR /usr/local/
 
-RUN pip install --upgrade pip && pip install \
-    numpy \
-    pyomo \
-    pysam \
-    matplotlib \
-    tables \
-    pandas \
-    future
-    
+
+RUN apt-get update && apt-get install -y python-setuptools python3-dev build-essential python3-pip && apt-get clean && apt-get purge
+
+# pip install --upgrade pip &&
+RUN pip3 install \
+    numpy==1.10.0 \
+    tables==3.2.2 \
+    pysam==0.8.3 \
+    future==0.15.2 \
+    pyomo==4.2.10782 \
+    pandas==0.23.0
+
+RUN pip3 install matplotlib==1.4.3
+
+# 虽然官方指出 Pandas 0.16.2,但安装报错 RuntimeError: Python version >= 3.5 required, 解决: 安装 pandas==0.23.0  ref:https://zhuanlan.zhihu.com/p/76850433
+#     matplotlib==1.4.3 \
+# 同理numpy==1.9.3 执行时报错 numpy==1.10.0
+
 #installing optitype form git repository (version Dec 09 2015) and wirtig config.ini
 RUN git clone https://github.com/FRED-2/OptiType.git \
-    && sed -i -e '1i#!/usr/bin/env python\' OptiType/OptiTypePipeline.py \
+    && sed -i -e '1i#!/usr/bin/env python' OptiType/OptiTypePipeline.py \
     && mv OptiType/ /usr/local/bin/ \
     && chmod 777 /usr/local/bin/OptiType/OptiTypePipeline.py \
     && echo "[mapping]\n\
@@ -75,16 +90,27 @@ unpaired_weight=0 \n\
 use_discordant=false\n" >> /usr/local/bin/OptiType/config.ini
 
 #installing razers3
-RUN git clone https://github.com/seqan/seqan.git seqan-src \
-    && cd seqan-src \
+# git clone https://github.com/seqan/seqan.git seqan-src
+WORKDIR /opt
+RUN git clone https://github.com/seqan/seqan.git seqan-src
+RUN cd seqan-src \
     && cmake -DCMAKE_BUILD_TYPE=Release \
     && make razers3 \
-    && cp bin/razers3 /usr/local/bin \
+    && cp bin/razers3 /usr/local/bin/ \
     && cd .. \
     && rm -rf seqan-src
 
 ENV PATH=/usr/local/bin/OptiType:$PATH
 
+
+# Add user biodocker with password biodocker
+RUN mkdir /data /config
+RUN groupadd fuse && \
+    useradd --create-home --shell /bin/bash --user-group --uid 1000 --groups sudo,fuse biodocker && \
+    echo `echo "biodocker\nbiodocker\n" | passwd biodocker` && \
+    chown biodocker:biodocker /data && \
+    chown biodocker:biodocker /config
+
 # Change user to back to biodocker
 USER biodocker
 
@@ -92,10 +118,10 @@ USER biodocker
 WORKDIR /data/
 
 # Define default command
-ENTRYPOINT ["OptiTypePipeline.py"]
+ENTRYPOINT ["python3", "OptiTypePipeline.py"]
 CMD ["-h"]
 
 ##################### INSTALLATION END ##########################
-
 # File Author / Maintainer
 MAINTAINER Benjamin Schubert <schubert@informatik.uni-tuebingen.de>
+# modify by biolxy <biolxy@aliyun.com>
\ No newline at end of file