Gtnseq/Dockerfile
c363be7d920emaster

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			#FROM ubuntu:16.04
			FROM khturner/tn-seq

			MAINTAINER Diego Villamaina version: 0.1

			## Update repo list and install required packages ####
			RUN apt-get update -y && apt-get install -y \
			software-properties-common \
			time \
			libffi-dev \
			libssl-dev \
			git-core \
			apt-transport-https \
			wget \
			unzip \
			build-essential \
			python-dev \
			python3-pip \
			python2.7-dev \
			python-pip \
			python-numpy \
			python-matplotlib \
			python-pysam \
			trimmomatic

			## Install snakemake (Require python >= 3.5)
			RUN pip3 install snakemake

			## Gtnseq app
			COPY Snakefile Snakefile_Localhost gtn.py /gtn/

			## Cannot run pip install <package> gives: ImportError: cannot import name main
			RUN pip install --upgrade pip && \
			python -m pip install virtualenv

			###########################
			### Install gc3pie ########
			###########################
			#RUN wget https://raw.githubusercontent.com/uzh/gc3pie/master/install.py && \
			COPY install.py /root/
			RUN python /root/install.py --develop -y

			## Install packages within gc3pie virtualenv
			RUN . /root/gc3pie/bin/activate && \
			pip install os-client-config \
			python-novaclient \
			python-neutronclient \
			python-openstackclient

			# Add gc3pie.conf file (my own conf for demo)
			COPY gc3pie.conf /root/.gc3/

			# Add SC auth file
			COPY enhancer.ch-openrc.sh run_gtn.sh /

			########################

			## Install FASTQC ###
			WORKDIR /opt
			RUN wget http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.8.zip && \
			unzip fastqc_v0.11.8.zip && \
			chmod 755 /opt/FastQC/fastqc && \
			rm /opt/fastqc_v0.11.8.zip

			###### Add tools PATHS to $PATH #########
			ENV PATH="/opt/FastQC/:${PATH}"

			ENTRYPOINT ["/run_gtn.sh"]

Gtnseq/Dockerfilec363be7d920emaster

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Gtnseq/Dockerfile
c363be7d920emaster

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