aaronmussig/gtdbtk repository overview

# Build
docker build --no-cache --tag aaronmussig/gtdbtk:latest .

# Test
docker run --rm -v /Volumes/128gb/gtdbtkout:/data -v /Volumes/128gb/release86:/refdata aaronmussig/gtdbtk gtdbtk test --out_dir /data/output

# Upload
docker tag aaronmussig/gtdbtk:latest aaronmussig/gtdbtk:0.2.2
docker push aaronmussig/gtdbtk:latest
docker push aaronmussig/gtdbtk:0.2.2

# DEBUG
docker run -it aaronmussig/gtdbtk /bin/bash

FROM ubuntu:18.04

# Install the required packages.
RUN apt-get update && \
    apt-get install -y --no-install-recommends wget ca-certificates unzip hmmer python2.7 python-pip python-setuptools python-numpy python-scipy python-matplotlib libgomp1 && \
    mkdir /data && \
    mkdir /refdata

# Install Prodigal.
WORKDIR /tmp
RUN wget https://github.com/hyattpd/Prodigal/releases/download/v2.6.3/prodigal.linux -q && \
    mv prodigal.linux /usr/bin/prodigal && \
    chmod +x /usr/bin/prodigal

# Install pplacer
WORKDIR /tmp
RUN wget https://github.com/matsen/pplacer/releases/download/v1.1.alpha19/pplacer-linux-v1.1.alpha19.zip -q && \
    unzip pplacer-linux-v1.1.alpha19.zip && \
    mv pplacer-Linux-v1.1.alpha19/* /usr/bin && \
    rm pplacer-linux-v1.1.alpha19.zip && \
    rm -rf pplacer-Linux-v1.1.alpha19

# Install FastANI
RUN wget https://github.com/ParBLiSS/FastANI/releases/download/v1.1/fastani-Linux64-v1.1.zip -q && \
    unzip fastani-Linux64-v1.1.zip -d /usr/bin && \
    rm fastani-Linux64-v1.1.zip

# Install FastTree
WORKDIR /usr/bin
RUN wget http://www.microbesonline.org/fasttree/FastTree -q && \
    wget http://www.microbesonline.org/fasttree/FastTreeMP -q

# Install GTDBTk
RUN pip install wheel future gtdbtk && \
    echo '#!/bin/bash \n python ~/.local/bin/gtdbtk $@' > /usr/bin/gtdbtk && \
    chmod +x /usr/bin/gtdbtk

# Export the GTDB-Tk data path
ENV GTDBTK_DATA_PATH="/refdata/"