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update to python3 in OptiType container #99

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78 changes: 52 additions & 26 deletions Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -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\
Expand All @@ -75,27 +90,38 @@ 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

# Change workdir to /data/
WORKDIR /data/

# Define default command
ENTRYPOINT ["OptiTypePipeline.py"]
ENTRYPOINT ["python3", "OptiTypePipeline.py"]
CMD ["-h"]

##################### INSTALLATION END ##########################

# File Author / Maintainer
MAINTAINER Benjamin Schubert <[email protected]>
# modify by biolxy <[email protected]>