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FROM adreeve/python-numpy:latest
ENV PATH /usr/local/bin:$PATH
RUN mkdir -p /home/progs
WORKDIR /home/progs
RUN apt-get update \
&& apt-get --yes install git ssh rsync nano graphviz \
wget zlibc zlib1g-dev unzip zip \
libncurses5-dev libncursesw5-dev libboost-dev \
python3-pip
RUN pip3 install snakemake pyyaml psutil
# python-software-properties\
# build-essential \
# python3-software-properties \
# software-properties-common \
# libncurses5-dev libncursesw5-dev libboost-dev
#docutils
## Gene-regulation
RUN wget https://github.com/rioualen/gene-regulation/archive/4.0.tar.gz && \
tar zvxf 4.0.tar.gz && \
ln -s gene-regulation-4.0 gene-regulation && \
rm 4.0.tar.gz
## Programs
# bowtie2
RUN wget --no-clobber http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.2.6/bowtie2-2.2.6-linux-x86_64.zip && \
unzip bowtie2-2.2.6-linux-x86_64.zip && \
cp `find bowtie2-2.2.6/ -maxdepth 1 -executable -type f` /usr/local/bin
# fastqc
RUN wget --no-clobber http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.5.zip && \
unzip -o fastqc_v0.11.5.zip && \
chmod +x FastQC/fastqc && \
cp FastQC/fastqc /usr/local/bin
# samtools
RUN wget --no-clobber http://sourceforge.net/projects/samtools/files/samtools/1.3/samtools-1.3.tar.bz2 && \
bunzip2 -f samtools-1.3.tar.bz2 && \
tar xvf samtools-1.3.tar && \
cd samtools-1.3 && \
make && \
sudo make install
WORKDIR /home/progs
# bedtools
RUN wget --no-clobber https://github.com/arq5x/bedtools2/releases/download/v2.24.0/bedtools-2.24.0.tar.gz && \
tar xvfz bedtools-2.24.0.tar.gz && \
cd bedtools2 && \
make && \
sudo make install
WORKDIR /home/progs
# macs2
RUN sudo pip install MACS2
# homer
RUN mkdir Homer && \
cd Homer && \
wget -nc "http://homer.salk.edu/homer/configureHomer.pl" && \
perl configureHomer.pl -install homer && \
cp `find bin/ -maxdepth 1 -executable -type f` /usr/local/bin
RUN pip3 install -U pandas
#RUN echo export SHELL=/bin/bash >> /root/.bashrc
#RUN echo export PATH=$PATH:/root/bin >> /root/.bashrc
MAINTAINER Claire Rioualen <claire.rioualen@inserm.fr>