text: # Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
  # Spack Project Developers. See the top-level COPYRIGHT file for details.
  #
  # SPDX-License-Identifier: (Apache-2.0 OR MIT)
  
  from spack import *
  
  
  class Trinity(MakefilePackage):
      """Trinity, developed at the Broad Institute and the Hebrew University of
         Jerusalem, represents a novel method for the efficient and robust de
         novo reconstruction of transcriptomes from RNA-seq data. Trinity
         combines three independent software modules: Inchworm, Chrysalis, and
         Butterfly, applied sequentially to process large volumes of RNA-seq
         reads. Trinity partitions the sequence data into many individual de
         Bruijn graphs, each representing the transcriptional complexity at a
         given gene or locus, and then processes each graph independently to
         extract full-length splicing isoforms and to tease apart transcripts
         derived from paralogous genes.
      """
  
      homepage = "http://trinityrnaseq.github.io/"
      url      = "https://github.com/trinityrnaseq/trinityrnaseq/archive/Trinity-v2.6.6.tar.gz"
  
      version('2.6.6', 'b7472e98ab36655a6d9296d965471a56')
  
      depends_on("java@8:", type=("build", "run"))
      depends_on("bowtie2")
      depends_on("jellyfish")
      depends_on("salmon")
      depends_on("perl+threads", type=("build", "run"))
      depends_on("autoconf", type="build")
      depends_on("automake", type="build")
      depends_on("libtool", type="build")
  
      # There is no documented list of these deps, but they're in the Dockerfile
      #  and we have runtime errors without them
      # https://github.com/trinityrnaseq/trinityrnaseq/blob/master/Docker/Dockerfile
      depends_on("blast-plus", type="run")
      depends_on("bowtie", type="run")
      depends_on("r", type="run")
      depends_on("r-tidyverse", type="run")
      depends_on("r-edger", type="run")
      depends_on("r-deseq2", type="run")
      depends_on("r-ape", type="run")
      depends_on("r-gplots", type="run")
      depends_on("r-biobase", type="run")
      depends_on("r-qvalue", type="run")
      depends_on("rsem", type="run")
      depends_on("kallisto", type="run")
      depends_on("fastqc", type="run")
      depends_on("samtools", type="run")
      depends_on("py-numpy", type="run")
      depends_on("express", type="run")
      depends_on("perl-dbfile", type="run")
      depends_on("perl-uri", type="run")
      depends_on("r-fastcluster", type="run")
      depends_on("r-ctc", type="run")
      depends_on("r-goseq", type="run")
      depends_on("r-glimma", type="run")
      depends_on("r-rots", type="run")
      depends_on("r-goplot", type="run")
      depends_on("r-argparse", type="run")
      depends_on("r-sm", type="run")
  
      def build(self, spec, prefix):
          make()
          make("trinity_essentials")
          make("plugins")
  
      def install(self, spec, prefix):
          install_tree('.', prefix.bin)
          force_remove(join_path(prefix.bin, '.gitmodules'))
          force_remove(join_path(prefix.bin, 'Butterfly', '.err'))
          force_remove(join_path(prefix.bin, 'Butterfly', 'src', '.classpath'))
          force_remove(join_path(prefix.bin, 'Butterfly', 'src', '.err'))
          force_remove(join_path(prefix.bin, 'Butterfly', 'src', '.project'))
          remove_linked_tree(join_path(prefix.bin, 'Butterfly', 'src',
                                       '.settings'))
          remove_linked_tree(join_path(prefix.bin, 'Inchworm', 'src', '.deps'))
          remove_linked_tree(join_path(prefix.bin, 'trinity-plugins',
                                       'ParaFly-0.1.0', 'src', '.deps'))
          force_remove(join_path(prefix.bin, 'trinity-plugins',
                                 'seqtk-trinity-0.0.2', '.gitignore'))
          force_remove(join_path(prefix.bin, 'trinity-plugins', 'slclust', 'bin',
                                 '.hidden'))
  
      def setup_environment(self, spack_env, run_env):
          run_env.set('TRINITY_HOME', self.prefix.bin)
          run_env.prepend_path('PATH', self.prefix.bin.util)
          spack_env.append_flags('CXXFLAGS', self.compiler.openmp_flag)
  