Installing Séance

Séance builds on multiple applications and python libraries to provide a complete analysis pipeline from raw data to visualisation. The easiest way to install Séance is to install the python code first, followed by the application dependencies as there is a handy subcommand to check your installation.

 

Installation of Python source
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Installation of Python source

Get the source distribution, untar it and cd into it:

 

curl -O http://wasabiapp.org/download/seance/Seance-0.11.tar.gz
tar xf Seance-0.11.tar.gz
cd Seance-0.11/

 

One of the python modules requires libffi, which is not handled by pip properly (at time of writing). The workaround for Ubuntu/Debian is to just install it manually using apt:
 

sudo apt-get install libffi-dev

 

Next use the setup script to install the Séance module, the main Séance application script and all python dependencies (everything assumes you are running Python 2.7.x):

 

sudo python setup.py install

 

If all went well, you should be able to run:

 

seance test

 

Here is an example of what you should see:

 

ajm@leviathan:~/Seance-0.11$ seance test
checking system for cluster command dependancies :
    pagan found.
    blastn (needed for --label) not found!

checking system for phylogeny command dependancies :
    pagan found.
    exonerate found.
    bppphysamp not found!

checking system for preprocess command dependancies :
    uchime (needed for --chimeras) not found!
    sff2fastq found.
    PyroDist (needed for --denoise) not found!
    FCluster (needed for --denoise) not found!
    PyroNoise (needed for --denoise) not found!

 

From here you must install any missing dependencies that you need.

 


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Mandatory dependencies:

Optional dependencies: