R7855/Dockerfile
e875c6b3d7b0master

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			FROM ubuntu:16.04

			MAINTAINER Diego Villamaina version: 0.2

			## Update repo list and install required packages ####
			RUN apt-get update -y && apt-get install -y \
			software-properties-common \
			git-core \
			apt-transport-https \
			wget \
			unzip \
			build-essential \
			time \
			libfindbin-libs-perl \
			libz-dev \
			libbz2-dev \
			liblzma-dev \
			zlib1g-dev \
			libncurses5-dev \
			libncursesw5-dev \
			libcurl4-openssl-dev \
			libxml2-dev \
			gfortran \
			g++ \
			libreadline6-dev \
			libx11-dev \
			libxt-dev \
			tk-dev \
			libpng12-dev \
			libjpeg-dev \
			libcairo2-dev \
			libarmadillo-dev \
			libarmadillo6 \
			libffi-dev \
			libssl-dev \
			docker.io \
			python-dev \
			python3-pip \
			python2.7-dev \
			python-pip \
			python-numpy \
			python-matplotlib \
			python-pysam \
			sortmerna \
			trimmomatic \
			bedtools

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

			## Grna app
			COPY Snakefile grna.py /grna/

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

			### Install R ###
			#WORKDIR /opt
			#ENV R_VERS=R-3.4.1

			#RUN wget https://cran.r-project.org/src/base/R-3/$R_VERS.tar.gz && \
			# tar -xzf $R_VERS.tar.gz && \
			# cd /opt/$R_VERS && \
			# ./configure && make && make install && \
			# rm /opt/$R_VERS.tar.gz

			## Install DESeq2 ###
			#RUN Rscript -e 'source("http://bioconductor.org/biocLite.R");library(BiocInstaller); biocLite("DESeq2", dep = TRUE)'


			############## STAR 2.6.0 ###############
			WORKDIR /opt
			RUN wget https://github.com/alexdobin/STAR/archive/2.6.0a.tar.gz && \
			tar -xzf 2.6.0a.tar.gz && \
			cd /opt/STAR-2.6.0a/source && \
			make STAR && \
			rm /opt/2.6.0a.tar.gz

			################ #Samtools 1.3.1# #########
			WORKDIR /opt
			RUN wget https://github.com/samtools/samtools/releases/download/1.2/samtools-1.2.tar.bz2 && \
			tar --bzip2 -xf samtools-1.2.tar.bz2 && \
			cd samtools-1.2 && \
			make && \
			make install && \
			rm /opt/samtools-1.2.tar.bz2

			###### Add tools PATHS to $PATH #########
			ENV PATH="/opt/STAR-2.6.0a/source/:/opt/FastQC/:${PATH}"

			######## sortmerna: Download the database and index it #####
			WORKDIR /usr/bin
			RUN /usr/share/sortmerna/rRNA_databases/scripts/fetch_rrna_data.sh && \
			mkdir -p /usr/share/sortmerna/rRNA_databases/index && \
			./indexdb_rna --ref /usr/share/sortmerna/rRNA_databases/silva-arc-16s-id95.fasta,/usr/share/sortmerna/rRNA_databases/index/silva-arc-16s-id95 && \
			./indexdb_rna --ref /usr/share/sortmerna/rRNA_databases/silva-arc-23s-id98.fasta,/usr/share/sortmerna/rRNA_databases/index/silva-arc-23s-id98 && \
			./indexdb_rna --ref /usr/share/sortmerna/rRNA_databases/silva-bac-16s-id90.fasta,/usr/share/sortmerna/rRNA_databases/index/silva-bac-16s-id90 && \
			./indexdb_rna --ref /usr/share/sortmerna/rRNA_databases/silva-bac-23s-id98.fasta,/usr/share/sortmerna/rRNA_databases/index/silva-bac-23s-id98 && \
			./indexdb_rna --ref /usr/share/sortmerna/rRNA_databases/silva-euk-18s-id95.fasta,/usr/share/sortmerna/rRNA_databases/index/silva-euk-18s-id95 && \
			./indexdb_rna --ref /usr/share/sortmerna/rRNA_databases/silva-euk-28s-id98.fasta,/usr/share/sortmerna/rRNA_databases/index/silva-euk-28s-id98 && \
			./indexdb_rna --ref /usr/share/sortmerna/rRNA_databases/rfam-5.8s-database-id98.fasta,/usr/share/sortmerna/rRNA_databases/index/rfam-5.8s-database-id98 && \
			./indexdb_rna --ref /usr/share/sortmerna/rRNA_databases/rfam-5s-database-id98.fasta,/usr/share/sortmerna/rRNA_databases/index/rfam-5s-database-id98

			ENTRYPOINT ["/run_grna.sh"]

R7855/Dockerfilee875c6b3d7b0master

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R7855/Dockerfile
e875c6b3d7b0master

Dockerfile
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