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Diffstat (limited to 'var/spack/repos/builtin/packages/trinity/package.py')
| -rw-r--r-- | var/spack/repos/builtin/packages/trinity/package.py | 91 |
1 files changed, 91 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/trinity/package.py b/var/spack/repos/builtin/packages/trinity/package.py new file mode 100644 index 0000000000..8e198113d7 --- /dev/null +++ b/var/spack/repos/builtin/packages/trinity/package.py @@ -0,0 +1,91 @@ +# Copyright 2013-2018 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-escape", 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) |