# This file created by conda-build 24.5.1
# meta.yaml template originally from:
# /Users/distiller/project/recipes/bbmap, last modified Wed Aug 21 04:42:13 2024
# ------------------------------------------------

package:
  name: bbmap
  version: '39.08'
source:
  sha256: 7250e170aabc6702fb5ea2724e9f9af03bb7085bef8b006a92309e44c3f32f22
  url: https://downloads.sourceforge.net/project/bbmap/BBMap_39.08.tar.gz
build:
  number: '0'
  run_exports:
    - bbmap >=39.8,<40.0a0
  string: h4ffbc93_0
requirements:
  build:
    - ca-certificates 2024.7.4 hf0a4a13_0
    - cctools_osx-arm64 986 h670d6a2_3
    - clang 16.0.6 default_h675cc0c_11
    - clang-16 16.0.6 default_h5c12605_11
    - clang_impl_osx-arm64 16.0.6 hc421ffc_19
    - clang_osx-arm64 16.0.6 h54d7cd3_19
    - clangxx 16.0.6 default_h675cc0c_11
    - compiler-rt 16.0.6 h3808999_2
    - compiler-rt_osx-arm64 16.0.6 h3808999_2
    - icu 75.1 hfee45f7_0
    - ld64_osx-arm64 711 h4c89ff5_3
    - libclang-cpp16 16.0.6 default_h5c12605_11
    - libcxx 18.1.8 h5a72898_4
    - libiconv 1.17 h0d3ecfb_2
    - libllvm16 16.0.6 haab561b_3
    - libxml2 2.12.7 h01dff8b_4
    - libzlib 1.3.1 hfb2fe0b_1
    - llvm-tools 16.0.6 haab561b_3
    - openssl 3.3.1 hfb2fe0b_2
    - sigtool 0.1.3 h44b9a77_0
    - tapi 1100.0.11 he4954df_0
    - xz 5.2.6 h57fd34a_0
    - zstd 1.5.6 hb46c0d2_0
  host:
    - bzip2 1.0.8 h99b78c6_7
    - c-ares 1.33.0 h99b78c6_0
    - ca-certificates 2024.7.4 hf0a4a13_0
    - htslib 1.20 ha435bb7_2
    - krb5 1.21.3 h237132a_0
    - libcurl 8.9.1 hfd8ffcc_0
    - libcxx 18.1.8 h5a72898_4
    - libdeflate 1.20 h93a5062_0
    - libedit 3.1.20191231 hc8eb9b7_2
    - libev 4.33 h93a5062_2
    - libnghttp2 1.58.0 ha4dd798_1
    - libssh2 1.11.0 h7a5bd25_0
    - libzlib 1.3.1 hfb2fe0b_1
    - ncurses 6.5 hb89a1cb_0
    - openjdk 22.0.1 h363fedd_1
    - openssl 3.3.1 hfb2fe0b_2
    - patchelf 0.18.0 h965bd2d_1
    - pbzip2 1.1.13 h8e2fd4a_2
    - samtools 1.20 hc9c1273_1
    - xz 5.2.6 h57fd34a_0
    - zstd 1.5.6 hb46c0d2_0
  run:
    - bzip2 >=1.0.8,<2.0a0
    - openjdk >=7.0
    - samtools >=1.20,<2.0a0
test:
  commands:
    - bbmap.sh -V 2>&1 | grep "BBMap" > /dev/null
    - bbmerge.sh -V 2>&1 | grep "BBMerge" > /dev/null
    - bbduk.sh -V 2>&1 | grep "BBDuk" > /dev/null
    - bbmask.sh -V 2>&1 | grep "BBMask" > /dev/null
    - bbnorm.sh --help 2>&1 | grep "BBNorm" > /dev/null
  files:
    - test.fa
    - testdatabase.fa
    - testexpected.sam
about:
  dev_url: https://sourceforge.net/projects/bbmap
  doc_url: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
  home: https://sourceforge.net/projects/bbmap
  license: UC-LBL license (see package)
  license_file: license.txt
  summary: BBMap is a short read aligner, as well as various other bioinformatic tools.
extra:
  additional-platforms:
    - linux-aarch64
    - osx-arm64
  copy_test_source_files: true
  final: true
  identifiers:
    - biotools:bbmap
    - doi:10.1371/journal.pone.0185056
    - usegalaxy-eu:bbtools_bbmap
  notes: 'BBMap is a series of Java programs, but they come with a number of custom

    wrapper shell scripts. Each of these is symlinked to the conda bin directory

    during install.

    '
