# This file created by conda-build 3.24.0
# meta.yaml template originally from:
# /opt/recipe, last modified Mon May 22 20:12:19 2023
# ------------------------------------------------

package:
  name: bbmap
  version: '39.01'
source:
  sha256: 98608da50130c47f3abd095b889cc87f60beeb8b96169b664bc9d849abe093e6
  url: http://downloads.sourceforge.net/project/bbmap/BBMap_39.01.tar.gz
build:
  number: '1'
  string: h92535d8_1
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_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
    - libsanitizer 12.2.0 h46fd767_19
    - libstdcxx-ng 12.2.0 h46fd767_19
    - sysroot_linux-64 2.12 he073ed8_15
  host:
    - _libgcc_mutex 0.1 conda_forge
    - _openmp_mutex 4.5 2_gnu
    - alsa-lib 1.2.8 h166bdaf_0
    - bzip2 1.0.8 h7f98852_4
    - c-ares 1.19.1 hd590300_0
    - ca-certificates 2023.5.7 hbcca054_0
    - cairo 1.16.0 hbbf8b49_1016
    - expat 2.5.0 hcb278e6_1
    - font-ttf-dejavu-sans-mono 2.37 hab24e00_0
    - font-ttf-inconsolata 3.000 h77eed37_0
    - font-ttf-source-code-pro 2.038 h77eed37_0
    - font-ttf-ubuntu 0.83 hab24e00_0
    - fontconfig 2.14.2 h14ed4e7_0
    - fonts-conda-ecosystem 1 0
    - fonts-conda-forge 1 0
    - freetype 2.12.1 hca18f0e_1
    - gettext 0.21.1 h27087fc_0
    - giflib 5.2.1 h0b41bf4_3
    - graphite2 1.3.13 h58526e2_1001
    - harfbuzz 7.3.0 hdb3a94d_0
    - htslib 1.17 h81da01d_2
    - icu 72.1 hcb278e6_0
    - keyutils 1.6.1 h166bdaf_0
    - krb5 1.20.1 h81ceb04_0
    - lcms2 2.15 haa2dc70_1
    - lerc 4.0.0 h27087fc_0
    - libcups 2.3.3 h36d4200_3
    - libcurl 8.1.0 h409715c_0
    - libdeflate 1.18 h0b41bf4_0
    - libedit 3.1.20191231 he28a2e2_2
    - libev 4.33 h516909a_1
    - libexpat 2.5.0 hcb278e6_1
    - libffi 3.4.2 h7f98852_5
    - libgcc-ng 12.2.0 h65d4601_19
    - libglib 2.76.2 hebfc3b9_0
    - libgomp 12.2.0 h65d4601_19
    - libiconv 1.17 h166bdaf_0
    - libjpeg-turbo 2.1.5.1 h0b41bf4_0
    - libnghttp2 1.52.0 h61bc06f_0
    - libpng 1.6.39 h753d276_0
    - libssh2 1.10.0 hf14f497_3
    - libstdcxx-ng 12.2.0 h46fd767_19
    - libtiff 4.5.0 ha587672_6
    - libuuid 2.38.1 h0b41bf4_0
    - libwebp-base 1.3.0 h0b41bf4_0
    - libxcb 1.15 h0b41bf4_0
    - libzlib 1.2.13 h166bdaf_4
    - ncurses 6.3 h27087fc_1
    - openjdk 17.0.3 h19c1b89_7
    - openssl 3.1.0 hd590300_3
    - pbzip2 1.1.13 0
    - pcre2 10.40 hc3806b6_0
    - pixman 0.40.0 h36c2ea0_0
    - pthread-stubs 0.4 h36c2ea0_1001
    - samtools 1.17 hd87286a_1
    - xorg-fixesproto 5.0 h7f98852_1002
    - xorg-inputproto 2.3.2 h7f98852_1002
    - xorg-kbproto 1.0.7 h7f98852_1002
    - xorg-libice 1.0.10 h7f98852_0
    - xorg-libsm 1.2.3 hd9c2040_1000
    - xorg-libx11 1.8.4 h8ee46fc_1
    - xorg-libxau 1.0.11 hd590300_0
    - xorg-libxdmcp 1.1.3 h7f98852_0
    - xorg-libxext 1.3.4 h0b41bf4_2
    - xorg-libxfixes 5.0.3 h7f98852_1004
    - xorg-libxi 1.7.10 h7f98852_0
    - xorg-libxrender 0.9.10 h7f98852_1003
    - xorg-libxtst 1.2.3 h7f98852_1002
    - xorg-recordproto 1.14.2 h7f98852_1002
    - xorg-renderproto 0.11.1 h7f98852_1002
    - xorg-xextproto 7.3.0 h0b41bf4_1003
    - xorg-xproto 7.0.31 h7f98852_1007
    - xz 5.2.6 h166bdaf_0
    - zlib 1.2.13 h166bdaf_4
    - zstd 1.5.2 h3eb15da_6
  run:
    - bzip2 >=1.0.8,<2.0a0
    - libgcc-ng >=12
    - openjdk >=7.0
    - pbzip2
    - samtools
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:
  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:
  copy_test_source_files: true
  final: true
  identifiers:
    - biotools:bbmap
    - doi:10.1371/journal.pone.0185056
  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.

    '
