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
External tools
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.
External tools
Mandatory dependencies:
Optional dependencies:
- Ampliconnoise (if using the –denoise option)
- sff2fastq (needed for raw 454 data)
- UCHIME (if using the –chimeras option)