Conda
See the ‘activating the conda environment’ section below to access this
software.
Configuration required
See the relevant section below to configure this software before use.
funannotate-1.8.14
funannotate is a pipeline for genome annotation (built specifically for fungi,
but will also work with higher eukaryotes). Installation, usage, and more
information can be found at http://funannotate.readthedocs.io
Configuring the conda environment
In order to use augustus with this software, you need to run the
/local/cluster/conda/setup_funannotate_config.sh script and provide a path
for the augustus config to get copied to such that you can write to the
directory.
Then, you can run the command printed to the screen to activate the
environment, or check out a node with qrsh and run
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bash
source ~/activate_funannotate.sh
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To use over SGE, include the above source command in your shell script prior
to your funannotate commands.
Location and version
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$ source ~/activate_funannotate.sh
$ which funannotate
/local/cluster/funannotate-1.8.14/bin/funannotate
$ funannotate --version
funannotate v1.8.14
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The database location should be set for you automatically:
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$ echo $FUNANNOTATE_DB
/nfs1/CGRB/databases/funannotate/current
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Please contact me if you need any additional
configuration.
help message
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$ funannotate --help
Usage: funannotate <command> <arguments>
version: 1.8.14
Description: Funannotate is a genome prediction, annotation, and comparison pipeline.
Commands:
clean Find/remove small repetitive contigs
sort Sort by size and rename contig headers
mask Repeatmask genome assembly
train RNA-seq mediated training of Augustus/GeneMark
predict Run gene prediction pipeline
fix Fix annotation errors (generate new GenBank file)
update RNA-seq/PASA mediated gene model refinement
remote Partial functional annotation using remote servers
iprscan InterProScan5 search (Docker or local)
annotate Assign functional annotation to gene predictions
compare Compare funannotated genomes
util Format conversion and misc utilities
setup Setup/Install databases
test Download/Run funannotate installation tests
check Check Python, Perl, and External dependencies [--show-versions]
species list pre-trained Augustus species
database Manage databases
outgroups Manage outgroups for funannotate compare
Written by Jon Palmer (2016-2022) nextgenusfs@gmail.com with contributions by Jason Stajich jasonstajich.phd@gmail.com
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software ref: <>
research ref: <>