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trinity: full dependencies (#9064)

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Levi Baber 2018-09-04 14:35:06 -05:00 committed by Adam J. Stewart
parent 059daa2012
commit 5737155dd0
1 changed files with 31 additions and 0 deletions
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31
var/spack/repos/builtin/packages/trinity/package.py
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@ -52,6 +52,36 @@ class Trinity(MakefilePackage):
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")
@ -76,4 +106,5 @@ def install(self, spec, prefix):
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)