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BHNtools edited this page Oct 3, 2017 · 4 revisions

docker-ete

Debian(Stretch) docker image for ETE3.

I. What is this?

Debian(Stretch) docker image for phylogeny tree vizualisation.

    -Examples:
  • Default ncbi tree : pngs/ncbi-default-tree.png 
    • cut -f1 /home/najlabioinfo/species.txt | ete3 ncbiquery --tree | xvfb-run ete3 view --ncbi --image ncbi-default-tree.png
  • Colored tree: pngs/ncbi-colored-tree.png 
    • cut -f1 /home/najlabioinfo/species.txt | ete3 ncbiquery --tree | xvfb-run ete3 view -t --face 'value:@name, size:18, color:auto()' --face 'value:@dist, size:10' --image ncbi-colored-tree.png

    II. How to use it?

    a)Pull the image 

    docker pull bhntools/dockerete:latest

    b)Run the image 

    docker run -it bhntools/dockerete:latest ete3 -h

    c)Link

    https://hub.docker.com/r/bhntools/dockerete/

    III. References

    III.1/ Documentation

    III.2/ Support

    - docker-ete is a heavy, but complete, version. A smaller versions can be used :

      - Available version(without taxa-dump)
    • https://hub.docker.com/r/cbcrg/ete3/ : docker pull cbcrg/ete3

      - Create one in 10min
      apt-get install xvfb
       
      wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O Miniconda-latest-Linux-x86_64.sh
       
      bash Miniconda-latest-Linux-x86_64.sh -b -p ~/anaconda_ete/
       
      export PATH=~/anaconda_ete/bin:$PATH;
       
      conda install -c etetoolkit ete3 ete3_external_apps 
      xvfb-run ete3 view -t '(a, b); ' -o test.png

    III.3/ Bugs

    IV. Issues and Contributing

    IV.1/ Support

    If you are having issues, please let me know.

    IV.2/ Contribute

    Bug reports, bug fixes, and new features are always welcome.
    * Issue Tracker: github
    * Source Code: github

    IV.3/ Authors and Maintainers

    BEN HASSINE NAJLA : [email protected]

    BHNtools©2017
    MIT License.
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