about:
  home: 'https://github.com/trinityrnaseq/trinityrnaseq'
  license: "https://raw.githubusercontent.com/trinityrnaseq/trinityrnaseq/master/LICENSE.txt"
  summary: "Trinity assembles transcript sequences from Illumina RNA-Seq data"
build:
  number: 6
package:
  name: trinity
  version: 'date.2011_11_26'
source:
  md5: 3a4c4691908d37042ca63ca469c75fd3
  url: http://sourceforge.net/projects/trinityrnaseq/files/trinityrnaseq_r2011-11-26.tgz
  patches:
    - RunButterfly.cc.patch # this file is missing a header include
    - Trinity.pl.patch # Trinity requires exactly Java 1.6, but works fine >1.6, so adjust to be more permissive
    - samtools_makefile.patch # patch samtools Makefile due to missing curses.h
requirements:
  build:
    - perl
    - {{ compiler('c') }}
    - java-jdk >=6
    - bzip2
    - zlib
    - ncurses
  run:
    - perl
    - java-jdk >=6
    - bzip2
    - zlib
    - ncurses
test:
  commands:
    # This version of Trinity does not have a quick function to exit 0
    # So at least check that we can compile the file
    - "$PREFIX/bin/Trinity-test &> /dev/null"

extra:
  notes: "Trinity version date.2011_11_26 relies on a custom wrapper script, symlinked to bin/: Trinity-runner.sh. This script changes the current working directory to that of the Trinity.pl perl script before calling Trinity, so relative paths work as expected (particularly for Trinity plugins). All arguments are passed to Trinity.pl (via $@)"
  identifiers:
    - biotools:trinity
