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# Start from the bitnami minideb image
#FROM bitnami/minideb:stretch
FROM ubuntu:18.04
# Install packages
RUN apt-get update && \
apt-get upgrade -y && \
apt-get install -y apt-utils apt-transport-https openssh-client \
git build-essential cmake python3 python3-pip \
wget bash
# Install pip packages
RUN pip3 install scikit-learn==0.22 imbalanced-learn==0.6.1
# Clone the repo
RUN mkdir /home/test/
WORKDIR /home/test/
RUN git clone --recursive https://github.com/eliza-m/LRRpredictor_v1
# Set environment variables
ENV HOME=/home/test/
ENV LRRpredictor_HOME=/home/test/LRRpredictor_v1
ENV RaptorX_HOME=/home/test/LRRpredictor_v1/RaptorX_Property_Fast
ENV HHSUITE_HOME=/home/test/LRRpredictor_v1/hh-suite
ENV MakeNoOfThreads=4
# Prepare Uniprot Download
RUN mkdir /uniprot20 && \
mkdir /uniprot20/uniprot20_2016_02
ENV UNIPROT20_PATH=/uniprot20
COPY download-uniprot.sh /download-uniprot.sh
COPY download-validation-set.sh /download-validation-set.sh
# Build HHsuite
WORKDIR /home/test/LRRpredictor_v1/hh-suite
RUN git checkout LRRpredictor && git pull
WORKDIR /home/test/LRRpredictor_v1/hh-suite/lib
RUN git clone https://github.com/eliza-m/ffindex_soedinglab.git ffindex
WORKDIR /home/test/LRRpredictor_v1/hh-suite/lib/ffindex
RUN git checkout 360e417
WORKDIR /home/test/LRRpredictor_v1/hh-suite/
RUN mkdir build && mkdir install
WORKDIR /home/test/LRRpredictor_v1/hh-suite/build
RUN cmake -DCMAKE_BUILD_TYPE=RelWithDebInfo -G "Unix Makefiles" -DCMAKE_INSTALL_PREFIX=../install ..
RUN make -j $MakeNoOfThreads
RUN make install
# Build RaptorX
WORKDIR /home/test/LRRpredictor_v1/RaptorX_Property_Fast/
RUN git checkout LRRpredictor && git pull
WORKDIR /home/test/LRRpredictor_v1/RaptorX_Property_Fast/source_code
RUN make -j $MakeNoOfThreads
WORKDIR /home/test/LRRpredictor_v1/RaptorX_Property_Fast
RUN perl setup.pl
WORKDIR /home/test/LRRpredictor_v1/RaptorX_Property_Fast/databases
RUN rm uniprot20 && \
ln -s /uniprot20/uniprot20_2016_02 uniprot20
# Download training data
WORKDIR /home/test/LRRpredictor_v1/fullTraining
RUN wget old.biochim.ro/ib/departments/strbiochem/LRRpred/fullTraining_pkls.tar.gz && \
tar -xzf fullTraining_pkls.tar.gz && \
mv fullTraining_pkls/* ./ && \
rm fullTraining_pkls.tar.gz && \
rmdir fullTraining_pkls
# Prepare the results folder
WORKDIR /home/test/LRRpredictor_v1
RUN mkdir results
WORKDIR /