# This file created by conda-build 3.24.0
# meta.yaml template originally from:
# /opt/recipe, last modified Tue May 30 20:50:39 2023
# ------------------------------------------------

package:
  name: gridss
  version: 2.13.2
source:
  sha256: 4d5651b1fc27928c0f76f1e8e7b90a74e6feae0c1cb9abea17fa2bd359f1d704
  url: https://github.com/PapenfussLab/gridss/releases/download/v2.13.2/gridss-2.13.2.tar.gz
build:
  number: '2'
  string: h50ea8bc_2
requirements:
  build:
    - _libgcc_mutex 0.1 conda_forge
    - _openmp_mutex 4.5 2_gnu
    - autoconf 2.71 pl5321h2b4cb7a_1
    - automake 1.16.5 pl5321ha770c72_0
    - binutils_impl_linux-64 2.39 he00db2b_1
    - binutils_linux-64 2.39 h5fc0e48_13
    - gcc_impl_linux-64 12.2.0 hcc96c02_19
    - gcc_linux-64 12.2.0 h4798a0e_13
    - kernel-headers_linux-64 2.6.32 he073ed8_15
    - ld_impl_linux-64 2.39 hcc3a1bd_1
    - libgcc-devel_linux-64 12.2.0 h3b97bd3_19
    - libgcc-ng 12.2.0 h65d4601_19
    - libgomp 12.2.0 h65d4601_19
    - libnsl 2.0.0 h7f98852_0
    - libsanitizer 12.2.0 h46fd767_19
    - libstdcxx-ng 12.2.0 h46fd767_19
    - m4 1.4.18 h516909a_1001
    - make 4.3 hd18ef5c_1
    - perl 5.32.1 2_h7f98852_perl5
    - sysroot_linux-64 2.12 he073ed8_15
  host:
    - _libgcc_mutex 0.1 conda_forge
    - _openmp_mutex 4.5 2_gnu
    - bzip2 1.0.8 h7f98852_4
    - c-ares 1.19.1 hd590300_0
    - ca-certificates 2023.5.7 hbcca054_0
    - htslib 1.17 h81da01d_2
    - keyutils 1.6.1 h166bdaf_0
    - krb5 1.20.1 h81ceb04_0
    - libcurl 8.1.2 h409715c_0
    - libdeflate 1.18 h0b41bf4_0
    - libedit 3.1.20191231 he28a2e2_2
    - libev 4.33 h516909a_1
    - libgcc-ng 12.2.0 h65d4601_19
    - libgomp 12.2.0 h65d4601_19
    - libnghttp2 1.52.0 h61bc06f_0
    - libssh2 1.10.0 hf14f497_3
    - libstdcxx-ng 12.2.0 h46fd767_19
    - libzlib 1.2.13 h166bdaf_4
    - ncurses 6.3 h27087fc_1
    - openssl 3.1.1 hd590300_0
    - xz 5.2.6 h166bdaf_0
    - zlib 1.2.13 h166bdaf_4
    - zstd 1.5.2 h3eb15da_6
  run:
    - bc
    - bcftools
    - bioconductor-structuralvariantannotation >=1.6
    - bwa >=0.7
    - entrez-direct
    - htslib >=1.17,<1.18.0a0
    - htslib >=1.17,<1.18.0a0
    - kraken2 >=2.1
    - libgcc-ng >=12
    - libzlib >=1.2.13,<1.3.0a0
    - ncurses >=6.3,<7.0a0
    - openjdk >=8
    - r-argparser
    - r-base >=4.0
    - r-stringdist
    - r-testthat
    - r-tidyverse
    - repeatmasker >=4.1.1
    - samtools >=1.14
    - zlib
test:
  commands:
    - gridss -h 2>&1 | grep 'Usage:'
    - gridsstools 2>&1 | grep 'Usage:'
    - gridss_annotate_vcf_kraken2 2>&1 | grep 'Usage:'
    - gridss_annotate_vcf_repeatmasker 2>&1 | grep 'Usage:'
    - gridss_extract_overlapping_fragments 2>&1 | grep 'Usage:'
    - virusbreakend 2>&1 | grep 'Usage:'
    - virusbreakend-build --help 2>&1 | grep 'Usage:'
    - gridss_somatic_filter --help 2>&1 | grep -i usage
    - CallVariants --help 2>&1 | grep 'USAGE:'
    - CollectGridssMetrics --help 2>&1 | grep 'USAGE:'
    - AnnotateVariantsKraken --help 2>&1 | grep 'USAGE:'
    - AnnotateVariantsRepeatMasker --help 2>&1 | grep 'USAGE:'
about:
  home: https://github.com/PapenfussLab/gridss
  license: GPL-3.0-only
  license_family: GPL
  summary: 'GRIDSS: the Genomic Rearrangement IDentification Software Suite'
extra:
  copy_test_source_files: true
  final: true
  identifiers:
    - biotools:gridss
    - doi:10.1101/gr.222109.117
    - doi:10.1186/s13059-021-02423-x
  notes: The package contains additional command line wrappers for the GRIDSS java-based
    utilities.
