jfroula/fungal-asm repository overview

FROM ubuntu:14.04
MAINTAINER Stephan Trong
LABEL version=1.0.0
LABEL description=""

# Install build tools
RUN apt-get update && apt-get install -y \
 build-essential \
 curl \
 dh-autoreconf \
 git \
 libhdf5-serial-dev \
 zlib1g-dev \
 libncurses5-dev \
 libncursesw5-dev \
 nano \
 unzip \
 vim \
 wget \
 gawk \
 --force-yes && \
 apt-get autoclean && \
 apt-get autoremove -y

# Install bwa
RUN apt-get install -y bwa

# Install perl
RUN cd /opt && wget http://www.cpan.org/src/5.0/perl-5.26.1.tar.gz && \
 tar -xzf perl-5.26.1.tar.gz &&  \
 cd perl-5.26.1 && \
 ./Configure -des && \
 make && \
 make test && \
 make install && \
 rm -rf /opt/perl-5.26.1.tar.gz

# Install perl modules
RUN cpan install File::Slurp && \
 cpan install CWD && \
 cpan install YAML && \
 cpan install YAML:XS

# Install miniconda
RUN wget https://repo.anaconda.com/miniconda/Miniconda2-latest-Linux-x86_64.sh && \
 bash ./Miniconda2-latest-Linux-x86_64.sh -b

ENV PATH /root/miniconda2/bin:$PATH

# Install conda python packages
RUN conda install -c anaconda pyyaml && \
 conda install -c jmcmurray json && \
 conda install -c bioconda pysam && \
 conda install -c anaconda requests && \
 conda install -c anaconda numpy && \
 conda install -c auto email && \
 conda install -c anaconda scipy && \
 conda install -c conda-forge biopython && \
 conda install -c anaconda pandas

# Install tools

# Install velvet
RUN conda install -c bioconda velvet=1.2.10

# Install pigz
RUN conda install -c anaconda pigz

# Install allpaths
RUN conda install -c biobuilds allpathslg

# Install bbtools
RUN conda install -c bioconda bbmap==38.68

# Install wgsim
RUN conda install -c bioconda wgsim

# Install blast+ 2.6.0
RUN cd /opt && \
 wget --no-check-certificate ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.6.0/ncbi-blast-2.6.0+-x64-linux.tar.gz && \
 tar -xvf ncbi-blast-2.6.0+-x64-linux.tar.gz && \
 ln -s /opt/ncbi-blast-2.6.0+/bin/* /usr/local/bin/ && \
 rm -rf ncbi-blast-2.6.0+-x64-linux.tar.gz

# Install Spades
RUN conda install -c bioconda spades==3.13.1

# Install R
RUN conda install -c conda-forge r==3.4.1

# Copy python/perl apps to image
COPY bin /app/bin
COPY lib /app/lib
COPY config /app/config

ENV PATH /app/bin:$PATH
ENV PYTHONPATH /app/lib:$PYTHONPATH