# 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 <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 

```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 <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
```

software ref: <>  
research ref: <>