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FunGAP: Fungal Genome Annotation Pipeline. FunGAP performs gene prediction on given genome assembly and RNA-seq reads.

Using

Use the module name fungap to discover versions available and to load the application.

FunGAP has been built as a Singularity image, so after loading the module and running the fungap command, you're actually starting the container image within which you call the related commands. For example:

Within an Interactive Session:

[]$ module load fungap/1.1.1
[]$ fungap
Singularity> 

Singularity> python /workspace/FunGAP/get_augustus_species.py --genus_name "Saccharomyces" --email_address my.address5@uwyo.edu
Validating input genus name...
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Within a Submitted Job

If you are submitting a job to the cluster, then you need to run the python command within the image, otherwise it will act as if you’re calling from outside of it:

For example:

fungap
FUNGAP_DIR=/workspace/FunGAP
python $FUNGAP_DIR/fungap.py

# Results in error:
python: can't open file '/workspace/FunGAP/fungap.py': [Errno 2] No such file or directory

Using:

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The is no fungap module, instead we install this locally within a project. If you wish to use this application please contact ARCC and we can install and provide further details on how to use.