Dockerfile-celery

FROM python:2.7

RUN apt-get update && apt-get install -y muscle fort77 gcc g++ xorg-dev libreadline-dev gfortran perlbrew dos2unix

# ncbi blast
# version 2.2.26 for blastpgp
WORKDIR /deps
RUN wget -q ftp://ftp.ncbi.nlm.nih.gov/blast/executables/legacy.NOTSUPPORTED/2.2.26/blast-2.2.26-x64-linux.tar.gz -P /deps ;\
    mkdir -p /deps/blast ;\
    tar zxf /deps/blast-2.2.26-x64-linux.tar.gz -C /deps/blast --strip-components=1 && rm -f /deps/blast-2.2.26-x64-linux.tar.gz


# Install R
WORKDIR /deps
RUN wget -q https://cran.rstudio.com/src/base/R-3/R-3.2.2.tar.gz -P /deps ;\
    tar xzf /deps/R-3.2.2.tar.gz && rm -f /deps/R-3.2.2.tar.gz ;\
    cd R-3.2.2 ;\
    ./configure && make && make install


# Install python modules
WORKDIR /usr/src/app/
ADD requirements.txt /usr/src/app/requirements.txt
RUN pip install --no-cache-dir -r requirements.txt


# Install R modules
WORKDIR /usr/src/app/
ADD install.R /usr/src/app/install.R
RUN Rscript install.R


# Install perl 5.8.5
RUN perlbrew init && perlbrew install --notest perl-5.8.5
RUN ln -sf /root/perl5/perlbrew/perls/perl-5.8.5/bin/perl /usr/bin/perl

# Install SeRenDip
WORKDIR /deps
COPY serendip.tar.gz /deps/serendip.tar.gz
RUN tar xzf serendip.tar.gz && rm -f serendip.tar.gz
RUN find serendip -type d -exec touch \{\}/__init__.py \;

# Copy python code
WORKDIR /usr/src/app
COPY serendip_api /usr/src/app/serendip_api
COPY tests /usr/src/app/tests

# Environment variables
ENV C_FORCE_ROOT true