PluMA: Plugin-Based Microbiome Analysis


  1. Be sure you have Mothur, Cytoscape, and SCons installed and in your system PATH. P-M16S is compatible with the newest versions of each, which as of this release are: Mothur 1.39.5, Cytoscape 3.6.0 and SCons 3.0.1
  2. Clone PluMA.
  3. If your R or Python installations are in non-standard locations, set appropriate environment variables in Section 2.2 of the User Guide.
  4. Change to the pipelines/ directory.
  5. Clone P-M16S.
  6. Change to the P-M16S/ directory.
  7. Run ./, to automatically clone the plugins you need.
  8. Change to the PluMA root directory.
  9. Run 'scons perl=0' to compile PluMA (P-M16S has no Perl plugins).
  10. Run './pluma pipelines/P-M16S/config.Early.txt' for the Early pipeline, and './pluma pipelines/P-M16S/config.Late.txt' for the Late pipeline.
Questions? Contact lead developer Trevor Cickovski.