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Dockerfile
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FROM ubuntu:18.04
MAINTAINER sminot@fredhutch.org
# Install prerequisites
ARG DEBIAN_FRONTEND=noninteractive
RUN apt update && \
apt-get install -y build-essential wget unzip python2.7 \
python-dev git python-pip bats awscli \
libcurl4-openssl-dev make gcc zlib1g-dev curl
# Set the default langage to C
ENV LC_ALL C
# Use /share as the working directory
RUN mkdir /share
WORKDIR /share
# Add /scratch
RUN mkdir /scratch
# Folder for installation
RUN mkdir /usr/famli
# Install DIAMOND v0.9.10
RUN cd /usr/local/bin && \
wget -q https://github.com/bbuchfink/diamond/releases/download/v0.9.22/diamond-linux64.tar.gz && \
tar xzf diamond-linux64.tar.gz && \
rm diamond-linux64.tar.gz
# Install the SRA toolkit
RUN cd /usr/local/bin && \
wget -q https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.8.2/sratoolkit.2.8.2-ubuntu64.tar.gz && \
tar xzf sratoolkit.2.8.2-ubuntu64.tar.gz && \
ln -s /usr/local/bin/sratoolkit.2.8.2-ubuntu64/bin/* /usr/local/bin/ && \
rm sratoolkit.2.8.2-ubuntu64.tar.gz
# Install the FASTX Toolkit
RUN cd /usr/local/bin && \
wget -q http://hannonlab.cshl.edu/fastx_toolkit/fastx_toolkit_0.0.13_binaries_Linux_2.6_amd64.tar.bz2 && \
tar xf fastx_toolkit_0.0.13_binaries_Linux_2.6_amd64.tar.bz2 && \
rm fastx_toolkit_0.0.13_binaries_Linux_2.6_amd64.tar.bz2 && \
mv bin/* ./
# Install FAMLI from PyPI
RUN pip install famli==1.2 bucket_command_wrapper==0.3.0
# Add the local directory to the container
ADD . /usr/famli
# Add the taxonomic analysis script to the PATH
RUN ln -s /usr/famli/diamond-tax.py /usr/local/bin/
# Run tests and then remove the folder
RUN bats /usr/famli/tests/ && rm -r /usr/famli/tests/