Modifications to run PinAPL-py using Docker version 2.9.2

Dockerfile

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+FROM ubuntu:14.04
+
+### File author / maintainer
+MAINTAINER Olivier Harismendy "oharismendy@ucsd.edu"
+
+### change a working directory to /opt #######
+WORKDIR /opt
+
+### install
+RUN apt-get update && apt-get install -y \
+autoconf \
+build-essential \
+curl \
+git \
+g++ \
+gzip \
+libncurses5-dev \
+libssl-dev \
+libboost-all-dev \
+libbz2-dev \
+libfreetype6-dev \
+make \
+man \
+pkg-config \
+python \
+python-tk \
+python-pip \
+python-dev \
+python-numpy \
+python-yaml \
+software-properties-common \
+screen \
+samtools \
+vim \
+wget \
+zip \
+zlibc \
+zlib1g \
+zlib1g-dev \
+gedit \
+gpicview \
+r-base \
+default-jre
+
+RUN apt-get install liblzma-dev
+
+RUN R -e "install.packages(c('heatmap.2','gplots'), repos = 'http://cran.rstudio.com/')" 
+
+RUN pip install --upgrade pip &&\
+    pip install scipy \
+    statsmodels==0.6.1 \
+    pandas==0.19.1 \
+    matplotlib==2.0.2 \
+    joblib==0.9.4 \
+    numpy==1.11.2 \
+    Cython==0.25.2 \
+    pysam==0.10.0 \
+    xlrd==0.9.2 \
+    xlwt==0.7.5 \
+    openpyxl==1.7.0 \
+    multiqc==0.9 \
+    seaborn==0.9.0 \
+    multiprocessing && \ 
+    pip install --user --upgrade cutadapt
+
+
+RUN wget -O bowtie2.tar.gz --no-check-certificate https://github.com/BenLangmead/bowtie2/archive/v2.2.8.tar.gz &&\
+ tar -xzvf bowtie2.tar.gz &&\
+ cd bowtie2-2.2.8 &&\
+ make &&\
+ cp bowtie2 /usr/bin &&\
+ cp bowtie2-align-s /usr/bin &&\
+ cp bowtie2-align-l /usr/bin &&\
+ cp bowtie2-build /usr/bin &&\
+ cp bowtie2-build-s /usr/bin &&\
+ cp bowtie2-build-l /usr/bin &&\
+ cp bowtie2-inspect /usr/bin &&\
+ cp bowtie2-inspect-s /usr/bin &&\
+ cp bowtie2-inspect-l /usr/bin
+
+RUN wget --no-check-certificate http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.5.zip &&\
+	unzip fastqc_v0.11.5.zip &&\
+	ln -s /opt/FastQC/fastqc /usr/local/bin/fastqc &&\
+	chmod a+x /opt/FastQC/fastqc &&\
+	chmod a+x /usr/local/bin/*
+
+RUN git clone https://github.com/LewisLabUCSD/PinAPL-Py.git &&\
+	mkdir -p /workingdir &&\
+	mkdir -p /scratch &&\
+	chmod -R 755 /opt/PinAPL-Py/Scripts
+
+ENV PATH="/opt/PinAPL-Py/Scripts:/root/.local/bin/:${PATH}" 
+
+WORKDIR /workingdir