Updated dockerfile

Dockerfile

@@ -14,6 +14,8 @@
 # Run Cmd:          docker run -v /path/to/file/dir:/data fred2/optitype
 #################################################################
 
+ARG LATEST_VERSION="v1.3.4"
+
 # Source Image
 FROM biocontainers/biocontainers:latest
 
@@ -23,56 +25,34 @@ USER root
 # install
 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 \
+     python-pip \
+     python-sphinx \
+     python2.7 \
+     gcc-4.9 \
+     g++-4.9 \
+     coinor-cbc \
+     zlib1g-dev \
+     libbz2-dev \
+     libboost-dev \
 && 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 purge \
+&& pip install --upgrade pip
 
 #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/ \
-    && 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/
+    && 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
 
-RUN pip install --upgrade pip && pip install \
-    numpy \
-    pyomo \
-    pysam \
-    matplotlib \
-    tables \
-    pandas \
-    future
-
-#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 \
-    && mv OptiType/ /usr/local/bin/ \
-    && chmod 777 /usr/local/bin/OptiType/OptiTypePipeline.py \
-    && echo "[mapping]\n\
-razers3=/usr/local/bin/razers3 \n\
-threads=1 \n\
-\n\
-[ilp]\n\
-solver=cbc \n\
-threads=1 \n\
-\n\
-[behavior]\n\
-deletebam=true \n\
-unpaired_weight=0 \n\
-use_discordant=false\n" >> /usr/local/bin/OptiType/config.ini
+ENV LD_LIBRARY_PATH "/usr/local/lib:$LD_LIBRARY_PATH"
+ENV HDF5_DIR "/usr/local/"
 
 #installing razers3
 RUN git clone https://github.com/seqan/seqan.git seqan-src \
@@ -83,18 +63,28 @@ RUN git clone https://github.com/seqan/seqan.git seqan-src \
     && cd .. \
     && rm -rf seqan-src
 
-ENV PATH=/usr/local/bin/OptiType:$PATH
+#installing optitype form git repository (version Dec 09 2015) and wirtig config.ini
+RUN mkdir /usr/local/bin/OptiType/
+COPY ./ /usr/local/bin/OptiType/
+ENV PATH="/usr/local/bin/OptiType:$PATH"
+
+# Install modules locally
+RUN pip2 install --upgrade pip \
+    && pip2 install \
+         numpy \
+         pyomo \
+         pysam \
+         matplotlib \
+         tables \
+         pandas \
+         future
 
 # Change user to back to biodocker
 USER biodocker
 
 # Change workdir to /data/
 WORKDIR /data/
 
-# Define default command
-ENTRYPOINT ["OptiTypePipeline.py"]
-CMD ["-h"]
-
 ##################### INSTALLATION END ##########################
 
 # File Author / Maintainer

OptiTypePipeline.py

@@ -1,5 +1,6 @@
-#!/usr/bin/env python
+#!/usr/bin/env python2
 # coding=utf-8
+
 """
 ###################################################################
 
@@ -96,6 +97,7 @@
                         be written
   --verbose, -v         Set verbose mode on.
 """
+
 from __future__ import print_function
 from future import standard_library
 standard_library.install_aliases()

config.ini

@@ -0,0 +1,12 @@
+[mapping]
+razers3=/usr/local/bin/razers3
+threads=1
+
+[ilp]
+solver=cbc
+threads=1
+
+[behavior]
+deletebam=true
+unpaired_weight=0
+use_discordant=false