ReproPhylo

ReproPhylo, a reproducible phylogenetics pipeline

This Dockerfile is an extension of the Ipython-notebook Dockerfile. Thanks to the MAINTAINER IPython Project ipython-dev@scipy.org.

Installation without Docker

The following instructions have Ubuntu in mind. Following them will download RAxML, TrimAl, exonerate and BayesTraits from the Dockerfile repository and will put their directory in PATH. If they are already installed on your system you can skip this step. The same directory will be included in PYTHONPATH, as it has the ReproPhylo scripts.

Update you system

sudo apt-get update -y
sudo apt-get upgrade -y
sudo apt-get update -y -qq --fix-missing

Python and IPython dependencies

sudo apt-get install -y -q build-essential make gcc zlib1g-dev git python\
python-dev python-pip
sudo apt-get install -y -q libzmq3-dev sqlite3 libsqlite3-dev pandoc\
libcurl4-openssl-dev nodejs

Jupyter notebook

sudo pip install ipython[notebook]
sudo pip install --upgrade ipython[notebook]

Git

sudo apt-get install git

Biopython

sudo apt-get install python-setuptools python-numpy python-qt4\
python-scipy python-mysqldb python-lxml -y
sudo apt-get install python-biopython -y

ReproPhylo

sudo pip install reprophylo

ETE2

sudo pip install -q ete2

Dendropy

sudo pip install -q dendropy

Pandas

sudo pip install pandas

matplotlib

sudo apt-get build-dep python-matplotlib -y
sudo apt-get install python-matplotlib -y

mafft

sudo apt-get install mafft -y

muscle

sudo apt-get install muscle -y

RAxML, phylobayes, TrimAl, exonerate, BayesTraits, pal2nal

Any of the above can be installed into your path to be recognized by reprophylo.
If they are on your machine but not in your path, reprophylo allows you to specify the full path to the executable in your reprophylo script.

Or, you can follow these instructions to get them all installed:

Get the Dockerfile archive

cd ~
wget -c https://github.com/HullUni-bioinformatics/ReproPhyloDockerfile/archive/master.zip

Extract the archive

unzip master.zip
rm master.zip

Allow execution of binaries

cd ReproPhyloDockerfile-master
chmod a+x BayesTraitsV2 exonerate raxmlHPC raxmlHPC-PTHREADS-AVX\
raxmlHPC-PTHREADS-SSE3 readal trimal pb tracecomp bpcomp

Add to PATH and PYTHONPATH

echo 'export PATH="$PATH:~/ReproPhyloDockerfile-master"' >> ~/.bashrc
echo 'export PYTHONPATH="$PYTHONPATH:~/ReproPhyloDockerfile-master"' >> ~/.bashrc
source ~/.bashrc

You should now be able to start jupyter notebook with
ipython notebook
in any location and use reprophylo as described in the manual