# This file created by conda-build 3.21.8
# meta.yaml template originally from:
# /opt/recipe, last modified Tue Mar  7 03:46:50 2023
# ------------------------------------------------

package:
  name: augustus
  version: 3.5.0
source:
  patches:
    - 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: '2'
  string: pl5321h816be78_2
requirements:
  build:
    - _libgcc_mutex 0.1 conda_forge
    - _openmp_mutex 4.5 2_gnu
    - binutils_impl_linux-64 2.39 he00db2b_1
    - binutils_linux-64 2.39 h5fc0e48_11
    - gcc_impl_linux-64 10.4.0 h5231bdf_19
    - gcc_linux-64 10.4.0 h9215b83_11
    - gxx_impl_linux-64 10.4.0 h5231bdf_19
    - gxx_linux-64 10.4.0 h6e491c6_11
    - kernel-headers_linux-64 2.6.32 he073ed8_15
    - ld_impl_linux-64 2.39 hcc3a1bd_1
    - libgcc-devel_linux-64 10.4.0 hd38fd1e_19
    - libgcc-ng 12.2.0 h65d4601_19
    - libgomp 12.2.0 h65d4601_19
    - libsanitizer 10.4.0 h5246dfb_19
    - libstdcxx-devel_linux-64 10.4.0 hd38fd1e_19
    - libstdcxx-ng 12.2.0 h46fd767_19
    - make 4.3 hd18ef5c_1
    - sysroot_linux-64 2.12 he073ed8_15
  host:
    - _libgcc_mutex 0.1 conda_forge
    - _openmp_mutex 4.5 2_gnu
    - bamtools 2.5.1 hd03093a_10
    - boost-cpp 1.74.0 h75c5d50_8
    - bzip2 1.0.8 h7f98852_4
    - c-ares 1.18.1 h7f98852_0
    - ca-certificates 2022.12.7 ha878542_0
    - gmp 6.2.1 h58526e2_0
    - gsl 2.7 he838d99_0
    - htslib 1.17 h6bc39ce_0
    - icu 70.1 h27087fc_0
    - keyutils 1.6.1 h166bdaf_0
    - krb5 1.20.1 hf9c8cef_0
    - libblas 3.9.0 5_h92ddd45_netlib
    - libcblas 3.9.0 5_h92ddd45_netlib
    - libcurl 7.87.0 h6312ad2_0
    - libdeflate 1.13 h166bdaf_0
    - libedit 3.1.20191231 he28a2e2_2
    - libev 4.33 h516909a_1
    - libgcc-ng 12.2.0 h65d4601_19
    - libgfortran-ng 12.2.0 h69a702a_19
    - libgfortran5 12.2.0 h337968e_19
    - libgomp 12.2.0 h65d4601_19
    - libhwloc 2.9.0 hd6dc26d_0
    - libiconv 1.17 h166bdaf_0
    - liblapack 3.9.0 5_h92ddd45_netlib
    - libnghttp2 1.51.0 hdcd2b5c_0
    - libnsl 2.0.0 h7f98852_0
    - libsqlite 3.40.0 h753d276_0
    - libssh2 1.10.0 haa6b8db_3
    - libstdcxx-ng 12.2.0 h46fd767_19
    - libxml2 2.10.3 h7463322_0
    - libzlib 1.2.13 h166bdaf_4
    - lp_solve 5.5.2.5 h14c3975_1001
    - metis 5.1.0 h58526e2_1006
    - mpfr 4.1.0 h9202a9a_1
    - ncurses 6.3 h27087fc_1
    - openssl 1.1.1t h0b41bf4_0
    - perl 5.32.1 2_h7f98852_perl5
    - perl-inc-latest 0.500 pl5321ha770c72_0
    - perl-module-build 0.4232 pl5321ha770c72_0
    - readline 8.1.2 h0f457ee_0
    - samtools 0.1.19 h20b1175_10
    - sqlite 3.40.0 h4ff8645_0
    - suitesparse 5.10.1 h9e50725_1
    - tbb 2021.8.0 hf52228f_0
    - xz 5.2.6 h166bdaf_0
    - zlib 1.2.13 h166bdaf_4
    - zstd 1.5.2 h3eb15da_6
  run:
    - bamtools >=2.5.1,<2.5.2.0a0
    - biopython
    - boost-cpp >=1.74.0,<1.74.1.0a0
    - cdbtools
    - diamond
    - gsl >=2.7,<2.8.0a0
    - htslib >=1.17,<1.18.0a0
    - libblas >=3.9.0,<4.0a0
    - libcblas >=3.9.0,<4.0a0
    - libgcc-ng >=12
    - libsqlite >=3.40.0,<4.0a0
    - libstdcxx-ng >=12
    - libzlib >=1.2.13,<1.3.0a0
    - lp_solve
    - perl >=5.32.1,<5.33.0a0 *_perl5
    - perl-app-cpanminus
    - perl-dbi
    - perl-file-which
    - perl-module-build =0.4232
    - perl-parallel-forkmanager
    - perl-scalar-list-utils
    - perl-yaml
    - sqlite >=3.40.0,<4.0a0
    - suitesparse >=5.10.1,<6.0a0
    - tar
    - ucsc-fatotwobit
    - ucsc-twobitinfo
    - zlib >=1.2.13,<1.3.0a0
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:
  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:
  copy_test_source_files: true
  final: true
  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.
