# This file created by conda-build 3.12.1
# meta.yaml template originally from:
# /Users/distiller/project/recipes/bbmap, last modified Tue Aug 21 00:41:07 2018
# ------------------------------------------------

package:
    name: bbmap
    version: '38.22'
source:
    patches:
        - 0001-changed-jni-makefiles-to-be-more-standards-compatibl.patch
    sha256: 7ee6165440efc5fcfd108416d041e00c7d89002bc1fabfeb74a9c175528c9dea
    url: http://downloads.sourceforge.net/project/bbmap/BBMap_38.22.tar.gz
build:
    number: '0'
    string: h470a237_0
requirements:
    build:
        - openjdk 8.0.144 zulu8.23.0.3_2
        - toolchain 2.1.6 0
        - toolchain_c_osx-64 2.1.6 0
    run:
        - openjdk >=7.0
test:
    commands:
        - bbmap.sh -V 2>&1 | grep "BBMap" > /dev/null
        - bbmap.sh -V 2>&1 | grep "Version 38.22" > /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.

        '
    recipe-maintainers:
        - notestaff
