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################################################
# Dockerfile to build OrthoFinder software
# Based on debian blast
################################################
# Set the base image to debian blast
FROM simonalpha/ncbi-blast-docker
LABEL version="1.1.8"
# Set noninterative mode
ENV DEBIAN_FRONTEND noninteractive
################## Update & upgrade ######################
ENV PACKAGES wget make gcc g++ mafft unzip python-pip python-dev libatlas-base-dev gfortran
RUN apt-get update -y
RUN apt-get install -y ${PACKAGES}
################# Numpy / Scipy install ########################
RUN pip install numpy
RUN pip install scipy
################# Fastree install ########################
ENV FASTTREE_URL http://www.microbesonline.org/fasttree/FastTree
RUN wget -P /usr/local/bin ${FASTTREE_URL}
################# MCL install ########################
ENV MCL_URL http://micans.org/mcl/src/mcl-14-137.tar.gz
ENV MCL_PATH /opt/mcl-14-137
WORKDIR /opt
RUN wget ${MCL_URL} -O - | tar xvzf -
WORKDIR ${MCL_PATH}
RUN ./configure --prefix=/usr/local && make install
################# DLCpar install ########################
ENV DLCPAR_URL https://www.cs.hmc.edu/~yjw/software/dlcpar/pub/sw/dlcpar-1.0.tar.gz
ENV DLCPAR_PATH /opt/dlcpar-1.0
WORKDIR /opt
RUN wget ${DLCPAR_URL} --no-check-certificate -O - | tar zxvf -
WORKDIR ${DLCPAR_PATH}
RUN python setup.py install
################ FastME install ##########################
ENV FASTME_URL http://www.atgc-montpellier.fr/download/sources/fastme/fastme-2.1.5.tar.gz
ENV FASTME_PATH fastme-2.1.5
WORKDIR /opt
RUN wget ${FASTME_URL} --no-check-certificate -O - | tar zxvf -
WORKDIR ${FASTME_PATH}
RUN ./configure --prefix=/usr/local && make install
################# DIAMOND install ########################
ENV DIAMOND_URL https://github.com/bbuchfink/diamond/releases/download/v0.9.9/diamond-linux64.tar.gz
WORKDIR /opt
RUN wget ${DIAMOND_URL} --no-check-certificate -O - | tar xvzf - && mv diamond /usr/local/bin/diamond-sse2
########################### orthoFinder install & run tests #############################
ENV ORTHOFINDER_URL https://github.com/davidemms/OrthoFinder/archive/1.1.8.zip
ENV ORTHOFINDER_FILE_NAME 1.1.8.zip
ENV ORTHOFINDER_PATH /opt/OrthoFinder-1.1.8/orthofinder
WORKDIR /opt
RUN wget ${ORTHOFINDER_URL} --no-check-certificate && unzip ${ORTHOFINDER_FILE_NAME}
ENV PATH "$PATH:${ORTHOFINDER_PATH}"
WORKDIR /root
RUN pwd && ls -1
RUN orthofinder.py -f ${ORTHOFINDER_PATH}/ExampleDataset/
########################## clean source file #################################
RUN rm -r /opt/1.1.8.zip
###############################################################
MAINTAINER Monjeaud Cyril <Cyril.Monjeaud@irisa.fr>