Ubuntu-based image with PhyloSD: a pipeline for Phylogenomic Subgenome Detection
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This repository distributes a Docker image with ALLOPOLYPLOIDS ready to use.
See instructions here.
Once Docker is set up, you can run the image by typing this in the terminal:
docker run --rm -it eeadcsiccompbio/allopolyploids:latest /bin/bash
This might take a couple of minutes the first time as the image needs to be downloaded. Once the session starts, you will be logged in as user 'you' in directory '/home/you/'. Software packages are installed at '/allopolyploids'.
IMPORTANT: When the image is shut down any files created will be lost. Hence, input files and results should be stored in a local, persistent folder. This can be achieved by booting the image with a mounted, writtable folder containing input data:
chmod -R a+w ./data_folder
docker run --rm -v ./data_folder:/data_folder -it eeadcsiccompbio/allopolyploids:latest /bin/bash
This data_folder will contain all the results produced while running the image.
Read the step-by-step protocol at ALLOPOLYPLOIDS to learn about the analyses that can be performed with these tools. Please add the preffix /allopolyploids/ to commands in the protocol if you use this container.
This is the Dockerfile used to build this image:
FROM ubuntu:16.04
FROM r-base:3.6.0
LABEL maintainer="[email protected]"
# Install OS dependencies
RUN apt-get update && apt-get install -y \
bash-completion \
libdb-dev \
parallel \
curl \
git \
wget \
r-base \
&& rm -rf /var/lib/apt/lists/*
RUN curl -L http://cpanmin.us | perl - App::cpanminus
# install optional R dependencies for get_homologues/plot_matrix_heatmap.sh
RUN R -e "install.packages( c('ape', 'gplots', 'dendextend', 'factoextra'), \
dependencies=TRUE, repos='http://cran.rstudio.com') #, repos='https://cloud.r-project.org')"
# clone allopolyploids
RUN cachebuster=b953b33 git clone https://github.com/eead-csic-compbio/allopolyploids.git
RUN cd allopolyploids && git pull
RUN cd allopolyploids && make install
RUN cd allopolyploids && make test
# add version name to image
ARG version
LABEL version=$version
RUN echo $version
# prepare user env
RUN useradd -ms /bin/bash you
USER you
WORKDIR /home/you
ENV PERL5LIB=/allopolyploids/bin/lib/perl5:$PERL5LIB
ENV PATH="/allopolyploids/scripts:${PATH}"
Content type
Image
Digest
Size
2.1 GB
Last updated
almost 5 years ago
docker pull eeadcsiccompbio/allopolyploids