{% set version = "3.3.3" %}
{% set sha256 = "2fc5f9fd2f0c3bba2924df42ffaf55b5c130228cea18efdb3b6dfab9efa8c9f4" %}

package:
  name: augustus
  version: {{ version }}

source:
  url: https://github.com/Gaius-Augustus/Augustus/archive/v{{ version }}.tar.gz
  sha256: {{ sha256 }}
  patches:
    - patches/bam2hints.makefile.patch
    - patches/bam2wig.makefile.patch
    - patches/compileSpliceCands.makefile.patch
    - patches/filterBam.makefile.patch
    - patches/filterBam.src.makefile.patch  # [linux]
    - patches/filterBam.src.makefile.patch.osx  # [osx]
    - patches/homGeneMapping.src.makefile.patch
    - patches/joingenes.makefile.patch
    - patches/utrrnaseq.src.patch
    - patches/utrrnaseq.patch
    - patches/src.makefile.patch

build:
  number: 11

requirements:
  build:
    - {{ compiler('c') }}
    - {{ compiler('cxx') }}
    - make
  host:
    - zlib
    - samtools ==0.1.19
    - bamtools
    - htslib
    - gsl
    - lp_solve
    - boost-cpp
    - sqlite
    - suitesparse
    - libblas
    - libcblas
    - perl
    - perl-module-build
  run:
    - zlib
    - boost-cpp
    - gsl
    - lp_solve
    - biopython <=1.77
    - perl
    - perl-app-cpanminus
    - perl-module-build
    - perl-yaml
    - perl-dbi
    - perl-scalar-list-utils
    - perl-file-which
    - perl-parallel-forkmanager
    - sqlite
    - suitesparse
    - cdbtools
    - diamond
    # Needed by bamToWig.py
    - ucsc-fatotwobit
    - ucsc-twobitinfo
    - bamtools

test:
  commands:
    - augustus --version
    - aa2nonred.pl --help 2>&1 | grep "aa2nonred.pl" > /dev/null
    - autoAug.pl --help
    - autoAugPred.pl --help
    - autoAugTrain.pl --help 2>&1 | grep "autoAugTrain.pl" > /dev/null
    - bam2hints --help
    - bam2wig 2>&1 | grep "bam2wig" > /dev/null
    - bedgraph2wig.pl
    - blat2gbrowse.pl --help 2>&1 | grep "blat2gbrowse.pl" > /dev/null
    - blat2hints.pl
    - cegma2gff.pl 2>&1 | grep "cegma2gff.pl" > /dev/null
    - checkParamArchive.pl
    - cleanDOSfasta.pl
    - clusterAndSplitGenes.pl --help
    - compileSpliceCands 2>&1 | grep "compileSpliceCands" > /dev/null
    - computeFlankingRegion.pl 2>&1 | grep "computeFlankingRegion.pl" > /dev/null
    - createAugustusJoblist.pl
    - del_from_prfl.pl --help 2>&1 | grep "del_from_prfl.pl" > /dev/null
    - evalCGP.pl
    - eval_dualdecomp.pl --help
    - eval_multi_gtf.pl --help 2>&1 | grep "eval_multi_gtf.pl" > /dev/null
    - exonerate2hints.pl
    - filterBam --help 2>&1 | grep "filterBam" > /dev/null
    - filterGenesIn_mRNAname.pl
    - filterGenesIn.pl
    - filterGenesOut_mRNAname.pl
    - filterGenes.pl
    - filterInFrameStopCodons.pl
    - filterMaf.pl --help 2>&1 | grep "filterMaf.pl" > /dev/null
    - filterPSL.pl --help
    - filterShrimp.pl --help
    - filterSpliceHints.pl
    - findGffNamesInFasta.pl --help 2>&1 | grep "file" > /dev/null
    - gbrowseold2gff3.pl --help 2>&1 | grep "gbrowseold2gff3.pl" > /dev/null
    - gbSmallDNA2gff.pl 2>&1 | grep "gbSmallDNA2gff.pl" > /dev/null
    - getAnnoFasta.pl
    - getLinesMatching.pl 2>&1 | grep "getLinesMatching.pl" > /dev/null
    - gff2gbSmallDNA.pl 2>&1 | grep "gff2gbSmallDNA.pl" > /dev/null
    - gffGetmRNA.pl
    - gp2othergp.pl --help 2>&1 | grep "gp2othergp.pl" > /dev/null
    - gtf2aa.pl 2>&1 | grep "gtf2aa.pl" > /dev/null
    - gtf2bed.pl --help 2>&1 | grep "gtf2bed.pl" > /dev/null
    - gtf2gff.pl --help 2>&1 | grep "gtf2gff.pl" > /dev/null
    - gth2gtf.pl 2>&1 | grep "gth2gtf.pl" > /dev/null
    - hal2maf_split.pl --help 2>&1 | grep "hal2maf_split.pl" > /dev/null
    - homGeneMapping --help 2>&1 | grep "homGeneMapping" > /dev/null
    - intron2exex.pl --help 2>&1 | grep "intron2exex.pl" > /dev/null
    - join_mult_hints.pl --help 2>&1 | grep "join_mult_hints.pl" > /dev/null
    - joingenes --help 2>&1 | grep "joingenes" > /dev/null
    - joinPeptides.pl 2>&1 | grep "joinPeptides.pl" > /dev/null
    - maf2conswig.pl --help 2>&1 | grep "maf2conswig.pl" > /dev/null
    - makeMatchLists.pl --help 2>&1 | grep "help" > /dev/null
    - makeUtrTrainingSet.pl 2>&1 | grep "makeUtrTrainingSet.pl" > /dev/null
    - maskNregions.pl
    - moveParameters.pl
    - msa2prfl.pl --help
    - new_species.pl
    - optimize_augustus.pl
    - opt_init_and_term_probs.pl 2>&1 | grep "open" > /dev/null
    - parseSim4Output.pl 2>&1 | grep "parseSim4Output.pl" > /dev/null
    - partition_gtf2gb.pl --help 2>&1 | grep "parition_gtf2gb.pl" > /dev/null
    - pasapolyA2hints.pl 2>&1 | grep "pasapolyA2hints.pl" > /dev/null
    - peptides2alternatives.pl 2>&1 | grep "peptides2alternatives.pl" > /dev/null
    - peptides2hints.pl 2>&1 | grep "peptides2hints.pl" > /dev/null
    - polyA2hints.pl
    - pslMap.pl 2>&1 | grep "pslMap.pl" > /dev/null
    - randomSplit.pl
    - ratewig.pl
    - rmRedundantHints.pl 2>&1 | grep "rmRedundantHints.pl" > /dev/null
    - runAllSim4.pl --help 2>&1 | grep "runAllSim4.pl" > /dev/null
    - samMap.pl
    - scipiogff2gff.pl 2>&1 | grep "scipiogff2gff.pl" > /dev/null
    - setStopCodonFreqs.pl 2>&1 | grep "setStopCodonFreqs.pl" > /dev/null
    - simpleFastaHeaders.pl 2>&1 | grep "simpleFastaHeaders.pl" > /dev/null
    - simplifyFastaHeaders.pl 2>&1 | grep "simplifyFastaHeaders.pl" > /dev/null
    - splitMfasta.pl
    - split_wiggle.pl
    - summarizeACGTcontent.pl 2>&1 | grep "summarizeACGTcontent.pl" > /dev/null
    - transMap2hints.pl
    - uniquePeptides.pl 2>&1 | grep "uniquePeptides.pl" > /dev/null
    - utrgff2gbrowse.pl --help 2>&1 | grep "utrgff2gbrowse.pl" > /dev/null
    - utrrnaseq --help
    - weedMaf.pl --help 2>&1 | grep "weedMaf.pl" > /dev/null
    - wigchoose.pl --help
    - writeResultsPage.pl
    - yaml2gff.1.4.pl --help 2>&1 | grep "yaml2gff.pl" > /dev/null
    - getAnnoFastaFromJoingenes.py --help
    - bamToWig.py --help | grep -Fq 'bamToWig.py'
    - compare_masking.pl --help | grep -Fq 'compare_masking'
    - merge_masking.pl --help | grep -Fq 'merge_masking.pl'
    - fix_in_frame_stop_codon_genes.py --help | grep -Fq 'fix_in_frame_stop_codon_genes.py'

about:
  home: http://bioinf.uni-greifswald.de/augustus/
  license: Artistic Licence
  license_family: Other
  license_file: "src/LICENSE.TXT"
  summary: 'AUGUSTUS is a gene prediction program for eukaryotes written by Mario
    Stanke and Oliver Keller. It can be used as an ab initio program, which means
    it bases its prediction purely on the sequence. AUGUSTUS may also incorporate
    hints on the gene structure coming from extrinsic sources such as EST, MS/MS,
    protein alignments and synthenic genomic alignments.'

extra:
  identifiers:
    - biotools:augustus
    - doi:10.1093/bioinformatics/btr010
    - usegalaxy-eu:augustus
  notes: "Builds with sqlite support are currently only available on Linux due to compile issues with macOS."
  skip-lints:
    - should_not_be_noarch_source
