dockerized Augustus

This is a hacky way to run/install augustus with docker. Why? Well I develop on Mac OSX and some features of Augustus stopped working when I upgraded computers to apple silicon, so this little repo will allow you to build a working Augustus docker image and then "spoof" the scripts so that you can put this in your PATH and it can be picked up by some other software, ie funannotate or funannotate2.

docker build -t augustus .

This command will install augustus in the docker image.

$ augustus

AUGUSTUS (3.5.0) is a gene prediction tool.
Sources and documentation at https://github.com/Gaius-Augustus/Augustus

usage:
augustus [parameters] --species=SPECIES queryfilename

'queryfilename' is the filename (including relative path) to the file containing the query sequence(s)
in fasta format.

SPECIES is an identifier for the species. Use --species=help to see a list.

parameters:
--strand=both, --strand=forward or --strand=backward
--genemodel=partial, --genemodel=intronless, --genemodel=complete, --genemodel=atleastone or --genemodel=exactlyone
  partial      : allow prediction of incomplete genes at the sequence boundaries (default)
  intronless   : only predict single-exon genes like in prokaryotes and some eukaryotes
  complete     : only predict complete genes
  atleastone   : predict at least one complete gene
  exactlyone   : predict exactly one complete gene
--singlestrand=true
  predict genes independently on each strand, allow overlapping genes on opposite strands
  This option is turned off by default.
--hintsfile=hintsfilename
  When this option is used the prediction considering hints (extrinsic information) is turned on.
  hintsfilename contains the hints in gff format.
--AUGUSTUS_CONFIG_PATH=path
  path to config directory (if not specified as environment variable)
--alternatives-from-evidence=true/false
  report alternative transcripts when they are suggested by hints
--alternatives-from-sampling=true/false
  report alternative transcripts generated through probabilistic sampling
--sample=n
--minexonintronprob=p
--minmeanexonintronprob=p
--maxtracks=n
  For a description of these parameters see section 2 of RUNNING-AUGUSTUS.md.
--proteinprofile=filename
  When this option is used the prediction will consider the protein profile provided as parameter.
  The protein profile extension is described in section 5 of RUNNING-AUGUSTUS.md.
--progress=true
  show a progressmeter
--gff3=on/off
  output in gff3 format
--predictionStart=A, --predictionEnd=B
  A and B define the range of the sequence for which predictions should be found.
--UTR=on/off
  predict the untranslated regions in addition to the coding sequence. This currently works only for a subset of species.
--noInFrameStop=true/false
  Do not report transcripts with in-frame stop codons. Otherwise, intron-spanning stop codons could occur. Default: false
--noprediction=true/false
  If true and input is in genbank format, no prediction is made. Useful for getting the annotated protein sequences.
--uniqueGeneId=true/false
  If true, output gene identifyers like this: seqname.gN
--/Testing/testMode=prepare, --/Testing/testMode=run, (disabled by default)
  prepare      : prepare a new minimal data set to test comparative Augustus
  intronless   : run prediction over some given minimal data set
  (*) a minimal data set is one retaining only the information need in prediction, usually very small (order of Mb) compared to full sequence data sets (ordet of Gb)

For a complete list of parameters, type "augustus --paramlist". A description of the important ones can be found in the file RUNNING-AUGUSTUS.md.