Public Repository

Last pushed: a month ago
Short Description
Ubuntu-based image with GET_HOMOLOGUES and GET_PHYLOMARKERS ready to be used.
Full Description

This repository distributes a Docker image with GET_HOMOLOGUES and GET_PHYLOMARKERS ready to use. These tools are developed and maintained by Pablo Vinuesa at CCG-UNAM and Bruno Contreras Moreira at EEAD-CSIC. Please see also our blog post describing this release, and the detailed installation instructions of the Docker environment on your machine and the hands-on-tutorial on running GET_HOMOLOGUES + GET_PHYLOMARKERS within a Docker container.

Installing Docker

See instructions here and here.
In old Windows systems you might have to use Docker Toolbox + VirtualBox.
See here how to run docker without 'sudo' in Linux.

Examples of use

Once Docker is set up, you can run the image by typing this in the terminal:


docker run --rm -it csicunam/get_homologues: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/'. Both software packages are installed at '/get_phylomarkers' and '/get_homologues'. You can check the installed GET_HOMOLOGUES version, and then turn off the image with these commands:


get_homologues.pl -v
exit

In case you need Pfam-A and/or SwissProt with GET_HOMOLOGUES, they can be installed for an open session with:


cd /get_homologues/
perl install.pl 

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, writable folder containing input genomes or cluster files in FASTA format, as detailed in the tutorial


chmod -R a+w ./data_folder
docker run --rm -v ./data_folder:/data_folder -it csicunam/get_homologues:latest /bin/bash

This data_folder will contain all the results produced while running the image.

Users should read the appropriate manuals (GET_HOMOLOGUES, GET_PHYLOMARKERS) to learn about the analyses that can be performed with these tools.

Dockerfile

This is the Dockerfile used to build this image:

FROM ubuntu:16.04
FROM r-base:3.5.1

LABEL maintainer="bcontreras@eead.csic.es"

# Install dependencies from repos: GD for graphics, libidn11 for BLAST+
RUN apt-get update && apt-get install -y \
  bc \
  curl \
  git \
  htop \
  libgd-gd2-perl \
  libidn11 \
  libpython2.7 \
  procps \
  wget \
  && rm -rf /var/lib/apt/lists/*
RUN curl -L http://cpanmin.us | perl - App::cpanminus
RUN cpanm Inline::C Inline::CPP

# clone get_phylomarkers and install required R packages (slow)
RUN cachebuster=b953b30 git clone https://github.com/vinuesa/get_phylomarkers.git
RUN cd get_phylomarkers && Rscript install_R_deps.R
RUN cd get_phylomarkers && git pull
RUN cd get_phylomarkers && chmod a+wr test_sequences

# clone get_homologues and get binaries
RUN cachebuster=b953b35 git clone https://github.com/eead-csic-compbio/get_homologues.git
RUN cd get_homologues && git pull
RUN cd get_homologues && perl install.pl no_databases
RUN cd get_homologues && chmod a+wr db

# 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 PATH="/get_homologues:${PATH}"
ENV PATH="/get_phylomarkers:${PATH}"
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csicunam