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To install AXIOME from source, see the included README.
If you do not wish to be on the bleeding edge, we have stable Ubuntu packages available.
Ubuntu users, in the terminal, can install AXIOME with the command:
sudo apt-add-repository ppa:neufeldlab/ppa && sudo apt-get update && sudo apt-get install axiome
If you wish to use Infernal for sequence alignment, an appropriate model must be specified with the INFERNAL_MODEL environment variable. The seed.16s.reference_model.sto file is recommended by QIIME. You can set the INFERNAL_MODEL environment variable with the command:
You can place this command in your ~/.bashrc file so it does not have to be run every session.
AXIOME uses several R libraries that are not installed by default. To install these libraries, we must first set a default CRAN repository in the Rprofile.site file (typically located in /etc/R/). For details on this, see the example Rprofile.site.
Once the Rprofile.site has been created and configured, you can install the R libraries by running:
In order to use PANDAseq, it must be installed on the system:
sudo apt-get install pandaseq
The above command assumes the apmasell PPA has been added to your repositories. Alternatively, PANDAseq can be compiled from source at: https://github.com/neufeld/pandaseq