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