# Funannotate 1.8.14 {{< admonition tip "Conda" true >}} See the 'activating the conda environment' section below to access this software. {{< /admonition >}} {{< admonition warning "Configuration required" true >}} See the relevant section below to configure this software before use. {{< /admonition >}} ## 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 ------------------------------------------------------------------------------- ## 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 ```console bash source ~/activate_funannotate.sh ``` To use over SGE, include the above source command in your shell script prior to your funannotate commands. ## Location and version ```console $ source ~/activate_funannotate.sh $ which funannotate /local/cluster/funannotate-1.8.14/bin/funannotate $ funannotate --version funannotate v1.8.14 ``` The database location should be set for you automatically: ```console $ echo $FUNANNOTATE_DB /nfs1/CGRB/databases/funannotate/current ``` Please contact [me](email:ed@cqls.oregonstate.edu) if you need any additional configuration. ## help message ```console $ funannotate --help Usage: funannotate 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 ``` software ref: <> research ref: <>