# This file created by conda-build 24.7.1
# meta.yaml template originally from:
# /Users/runner/work/bioconda-recipes/bioconda-recipes/recipes/augustus, last modified Tue Jul  8 03:42:54 2025
# ------------------------------------------------

package:
  name: augustus
  version: 3.5.0
source:
  patches:
    - patches/0001-Makefile.patch
    - patches/0002-sqliteDB.patch
    - patches/homGeneMapping.src.makefile.patch
    - patches/utrrnaseq.patch
  sha256: 5ed6ce6106303b800c5e91d37a250baff43b20824657b853ae04d11ad8bdd686
  url: https://github.com/Gaius-Augustus/Augustus/archive/v3.5.0.tar.gz
build:
  number: '8'
  run_exports:
    - augustus >=3.5.0,<4.0a0
  string: pl5321hcc4d041_8
requirements:
  build:
    - ca-certificates 2025.6.15 hbd8a1cb_0
    - cctools_osx-64 1010.6 hd19c6af_6
    - clang 18.1.8 default_h576c50e_10
    - clang-18 18.1.8 default_h3571c67_10
    - clang_impl_osx-64 18.1.8 h6a44ed1_25
    - clang_osx-64 18.1.8 h7e5c614_25
    - clangxx 18.1.8 default_heb2e8d1_10
    - clangxx_impl_osx-64 18.1.8 h4b7810f_25
    - clangxx_osx-64 18.1.8 h7e5c614_25
    - compiler-rt 18.1.8 h1020d70_1
    - compiler-rt_osx-64 18.1.8 hf2b8a54_1
    - icu 75.1 h120a0e1_0
    - ld64_osx-64 951.9 h33512f0_6
    - libclang-cpp18.1 18.1.8 default_h3571c67_10
    - libcxx 20.1.7 hf95d169_0
    - libcxx-devel 18.1.8 h7c275be_8
    - libiconv 1.18 h4b5e92a_1
    - libllvm18 18.1.8 default_h3571c67_5
    - liblzma 5.8.1 hd471939_2
    - libxml2 2.14.4 h8c082e5_0
    - libzlib 1.3.1 hd23fc13_2
    - llvm-tools 18.1.8 default_h3571c67_5
    - llvm-tools-18 18.1.8 default_h3571c67_5
    - make 4.4.1 h00291cd_2
    - ncurses 6.5 h0622a9a_3
    - openssl 3.5.1 hc426f3f_0
    - sigtool 0.1.3 h88f4db0_0
    - tapi 1300.6.5 h390ca13_0
    - zstd 1.5.7 h8210216_2
  host:
    - bamtools 2.5.3 h3af6988_0
    - boost-cpp 1.85.0 hfcd56d9_4
    - bzip2 1.0.8 hfdf4475_7
    - c-ares 1.34.5 hf13058a_0
    - ca-certificates 2025.6.15 hbd8a1cb_0
    - gmp 6.3.0 hf036a51_2
    - gsl 2.7 h93259b0_0
    - htslib 1.22 h9f635df_0
    - icu 75.1 h120a0e1_0
    - jsoncpp 1.9.6 h466cfd8_1
    - krb5 1.21.3 h37d8d59_0
    - libamd 3.3.3 ha5840a7_7100102
    - libblas 3.9.0 12_h972e302_netlib
    - libboost 1.85.0 hcca3243_4
    - libboost-devel 1.85.0 h2b186f8_4
    - libboost-headers 1.85.0 h694c41f_4
    - libbtf 2.3.2 hca54c18_7100102
    - libcamd 3.3.3 hca54c18_7100102
    - libcblas 3.9.0 12_h9cb3e3b_netlib
    - libccolamd 3.3.4 hca54c18_7100102
    - libcholmod 5.3.1 h7ea7d7c_7100102
    - libcolamd 3.3.4 hca54c18_7100102
    - libcurl 8.14.1 h5dec5d8_0
    - libcxsparse 4.4.1 h3868ee3_7100102
    - libcxx 20.1.7 hf95d169_0
    - libdeflate 1.24 hcc1b750_0
    - libedit 3.1.20250104 pl5321ha958ccf_0
    - libev 4.33 h10d778d_2
    - libgfortran 5.0.0 14_2_0_h51e75f0_103
    - libgfortran5 14.2.0 h51e75f0_103
    - libklu 2.3.5 hc7f8671_7100102
    - liblapack 3.9.0 12_h8d7f381_netlib
    - libldl 3.3.2 hca54c18_7100102
    - liblzma 5.8.1 hd471939_2
    - liblzma-devel 5.8.1 hd471939_2
    - libnghttp2 1.64.0 hc7306c3_0
    - libparu 1.0.0 hf1a04d7_7100102
    - librbio 4.3.4 hca54c18_7100102
    - libspex 3.2.3 hc5c4b0d_7100102
    - libspqr 4.3.4 h795628b_7100102
    - libsqlite 3.50.2 he7d56d0_0
    - libssh2 1.11.1 hed3591d_0
    - libsuitesparseconfig 7.10.1 h00e5f87_7100102
    - libumfpack 6.3.5 h0658b90_7100102
    - libzlib 1.3.1 hd23fc13_2
    - llvm-openmp 20.1.7 ha54dae1_0
    - lp_solve 5.5.2.11 h10d778d_0
    - metis 5.1.0 h3023b02_1007
    - mpfr 4.2.1 haed47dc_3
    - ncurses 6.5 h0622a9a_3
    - openssl 3.5.1 hc426f3f_0
    - perl 5.32.1 7_h10d778d_perl5
    - perl-inc-latest 0.500 pl5321h694c41f_0
    - perl-module-build 0.4234 pl5321h694c41f_1
    - readline 8.2 h7cca4af_2
    - samtools 1.22 ha21ef43_0
    - sqlite 3.50.2 h22fafd5_0
    - suitesparse 7.10.1 h033788e_7100102
    - xz 5.8.1 h357f2ed_2
    - xz-gpl-tools 5.8.1 h357f2ed_2
    - xz-tools 5.8.1 hd471939_2
    - zlib 1.3.1 hd23fc13_2
    - zstd 1.5.7 h8210216_2
  run:
    - bamtools >=2.5.3,<3.0a0
    - biopython
    - boost-cpp
    - cdbtools
    - diamond
    - gsl >=2.7,<2.8.0a0
    - htslib >=1.22,<1.23.0a0
    - libamd >=3.3.3,<4.0a0
    - libblas >=3.9.0,<4.0a0
    - libbtf >=2.3.2,<3.0a0
    - libcamd >=3.3.3,<4.0a0
    - libcblas >=3.9.0,<4.0a0
    - libccolamd >=3.3.4,<4.0a0
    - libcholmod >=5.3.1,<6.0a0
    - libcolamd >=3.3.4,<4.0a0
    - libcxsparse >=4.4.1,<5.0a0
    - libcxx >=18
    - libklu >=2.3.5,<3.0a0
    - libldl >=3.3.2,<4.0a0
    - libparu >=1.0.0,<2.0a0
    - librbio >=4.3.4,<5.0a0
    - libspex >=3.2.3,<4.0a0
    - libspqr >=4.3.4,<5.0a0
    - libsqlite >=3.50.2,<4.0a0
    - libsuitesparseconfig >=7.10.1,<8.0a0
    - libumfpack >=6.3.5,<7.0a0
    - libzlib >=1.3.1,<2.0a0
    - lp_solve
    - perl >=5.32.1,<5.33.0a0 *_perl5
    - perl-app-cpanminus
    - perl-dbi
    - perl-file-which
    - perl-module-build =0.4234
    - perl-parallel-forkmanager
    - perl-scalar-list-utils
    - perl-yaml
    - samtools >=1.22,<2.0a0
    - sqlite
    - suitesparse >=7.10.1,<8.0a0
    - tar
    - ucsc-fatotwobit
    - ucsc-twobitinfo
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
    - 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:
  dev_url: https://github.com/Gaius-Augustus/Augustus
  doc_url: https://github.com/Gaius-Augustus/Augustus/blob/v3.5.0/docs/RUNNING-AUGUSTUS.md
  home: https://bioinf.uni-greifswald.de/augustus
  license: Artistic License
  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:
  additional-platforms:
    - linux-aarch64
    - osx-arm64
  copy_test_source_files: true
  final: true
  identifiers:
    - biotools:augustus
    - doi:10.1093/bioinformatics/btr010
    - usegalaxy-eu:augustus
    - usegalaxy-eu:augustus
    - usegalaxy-eu:augustus_training
    - usegalaxy-eu:augustus_training
  notes: Builds with sqlite support are currently only available on Linux due to compile
    issues with macOS.
