Fungani: Difference between revisions
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Created page with "Category:SoftwareCategory:BiologyCategory:Phylogenetics {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|fungani}} |{{#vardefine:url|https://github.com/podo-gec/fungani}} <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> |{{#vardefine:conf|}} <!--CONFIGURATION--> |{{#vardefine:exe|1}} <!--ADDITIONAL INFO--> |{{#vardefine:job|}} <!--JOB SCRIPTS--> |{{#vardefine:policy|}} <!--POLICY--> |{{#vardefine:testing|}} <..." |
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Command line executable | Command line executable | ||
$ python -m fungani.cli -h | $ python -m fungani.cli -h | ||
usage: fungani [-h] [-t THRESHOLD] [-p PERCENT] [-w SIZE] [-g OVERLAP] [-j CPUS] [-o OUTDIR] [-u] [-c] | usage: fungani reference test [-h] [-t THRESHOLD] [-p PERCENT] [-w SIZE] [-g OVERLAP] [-j CPUS] [-o OUTDIR] [-u] [-c] | ||
GUI can be launched in an Open Ondemand terminal: | GUI can be launched in an Open Ondemand terminal: | ||
Latest revision as of 21:58, 4 March 2025
Description
FUNGANI: A BLAST-based program for analyzing Average Nucleotide Identity (ANI) between two fungal genomes, enables easy fungal species delimitation.
Environment Modules
Run module spider fungani to find out what environment modules are available for this application.
System Variables
- HPC_FUNGANI_DIR - installation directory
- HPC_FUNGANI_BIN - executable directory
- FUNGANI_DIR - github directory
Additional 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 reference test [-h] [-t THRESHOLD] [-p PERCENT] [-w SIZE] [-g OVERLAP] [-j CPUS] [-o OUTDIR] [-u] [-c]
GUI can be launched in an Open Ondemand terminal:
$ python -m fungani