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fungani

Description

fungani website

FUNGANI: A BLAST-based program for analyzing Average Nucleotide Identity (ANI) between two fungal genomes, enables easy fungal species delimitation. Modules system sets up the following environment variables for this module: * FUNGANI_DIR - github repository

Environment Modules

Run module spider fungani to find out what environment modules are available for this application.

Environment Variables

  • HPC_FUNGANI_DIR - installation directory
  • HPC_FUNGANI_BIN - executable directory

Additional Usage Information

Executables need to be run from the root of the github repository. Either copy $FUNGANI_DIR or clone from github, and cd into personal 'fungani' folder:

$ module load fungani/0.1.0
$ cp -r $FUNGANI_DIR /path/to/myfungani
$ cd /path/to/myfungani

Command line executable

$ python -m fungani.cli -h
usage: fungani [-h] [-t THRESHOLD] [-p PERCENT] [-w SIZE] [-g OVERLAP] [-j CPUS] [-o OUTDIR] [-u] [-c] reference test

GUI can be launched in an Open Ondemand terminal:

$ python -m fungani

Categories

Phylogenetics