111 lines
5.0 KiB
Python
111 lines
5.0 KiB
Python
##############################################################################
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# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
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# Produced at the Lawrence Livermore National Laboratory.
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#
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# This file is part of Spack.
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# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
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# LLNL-CODE-647188
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#
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# For details, see https://github.com/spack/spack
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# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
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#
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# This program is free software; you can redistribute it and/or modify
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# it under the terms of the GNU Lesser General Public License (as
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# published by the Free Software Foundation) version 2.1, February 1999.
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#
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# This program is distributed in the hope that it will be useful, but
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# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
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# conditions of the GNU Lesser General Public License for more details.
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#
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# You should have received a copy of the GNU Lesser General Public
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# License along with this program; if not, write to the Free Software
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# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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##############################################################################
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from spack import *
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class Trinity(MakefilePackage):
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"""Trinity, developed at the Broad Institute and the Hebrew University of
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Jerusalem, represents a novel method for the efficient and robust de
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novo reconstruction of transcriptomes from RNA-seq data. Trinity
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combines three independent software modules: Inchworm, Chrysalis, and
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Butterfly, applied sequentially to process large volumes of RNA-seq
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reads. Trinity partitions the sequence data into many individual de
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Bruijn graphs, each representing the transcriptional complexity at a
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given gene or locus, and then processes each graph independently to
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extract full-length splicing isoforms and to tease apart transcripts
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derived from paralogous genes.
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"""
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homepage = "http://trinityrnaseq.github.io/"
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url = "https://github.com/trinityrnaseq/trinityrnaseq/archive/Trinity-v2.6.6.tar.gz"
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version('2.6.6', 'b7472e98ab36655a6d9296d965471a56')
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depends_on("java@8:", type=("build", "run"))
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depends_on("bowtie2")
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depends_on("jellyfish")
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depends_on("salmon")
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depends_on("perl+threads", type=("build", "run"))
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depends_on("autoconf", type="build")
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depends_on("automake", type="build")
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depends_on("libtool", type="build")
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# There is no documented list of these deps, but they're in the Dockerfile
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# and we have runtime errors without them
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# https://github.com/trinityrnaseq/trinityrnaseq/blob/master/Docker/Dockerfile
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depends_on("blast-plus", type="run")
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depends_on("bowtie", type="run")
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depends_on("r", type="run")
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depends_on("r-tidyverse", type="run")
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depends_on("r-edger", type="run")
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depends_on("r-deseq2", type="run")
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depends_on("r-ape", type="run")
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depends_on("r-gplots", type="run")
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depends_on("r-biobase", type="run")
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depends_on("r-qvalue", type="run")
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depends_on("rsem", type="run")
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depends_on("kallisto", type="run")
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depends_on("fastqc", type="run")
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depends_on("samtools", type="run")
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depends_on("py-numpy", type="run")
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depends_on("express", type="run")
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depends_on("perl-dbfile", type="run")
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depends_on("perl-uri-escape", type="run")
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depends_on("r-fastcluster", type="run")
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depends_on("r-ctc", type="run")
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depends_on("r-goseq", type="run")
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depends_on("r-glimma", type="run")
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depends_on("r-rots", type="run")
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depends_on("r-goplot", type="run")
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depends_on("r-argparse", type="run")
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depends_on("r-sm", type="run")
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def build(self, spec, prefix):
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make()
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make("trinity_essentials")
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make("plugins")
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def install(self, spec, prefix):
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install_tree('.', prefix.bin)
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force_remove(join_path(prefix.bin, '.gitmodules'))
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force_remove(join_path(prefix.bin, 'Butterfly', '.err'))
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force_remove(join_path(prefix.bin, 'Butterfly', 'src', '.classpath'))
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force_remove(join_path(prefix.bin, 'Butterfly', 'src', '.err'))
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force_remove(join_path(prefix.bin, 'Butterfly', 'src', '.project'))
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remove_linked_tree(join_path(prefix.bin, 'Butterfly', 'src',
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'.settings'))
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remove_linked_tree(join_path(prefix.bin, 'Inchworm', 'src', '.deps'))
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remove_linked_tree(join_path(prefix.bin, 'trinity-plugins',
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'ParaFly-0.1.0', 'src', '.deps'))
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force_remove(join_path(prefix.bin, 'trinity-plugins',
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'seqtk-trinity-0.0.2', '.gitignore'))
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force_remove(join_path(prefix.bin, 'trinity-plugins', 'slclust', 'bin',
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'.hidden'))
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def setup_environment(self, spack_env, run_env):
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run_env.set('TRINITY_HOME', self.prefix.bin)
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run_env.prepend_path('PATH', self.prefix.bin.util)
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spack_env.append_flags('CXXFLAGS', self.compiler.openmp_flag)
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