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Overview

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...
...

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:

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

# Results in:
usage: fungap.py -g <genome_assembly> -12UA <trans_read_files> -o <output_dir> -a <augustus_species> -b <busco_dataset> -s <sister_proteome>
fungap.py: error: the following arguments are required: -g/--genome_assembly, -a/--augustus_species, -b/--busco_dataset, -s/--sister_proteome

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