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| author | Levi Baber <baberlevi@gmail.com> | 2018-09-04 14:35:06 -0500 |
|---|---|---|
| committer | Adam J. Stewart <ajstewart426@gmail.com> | 2018-09-04 14:35:06 -0500 |
| commit | 5737155dd0de1adc51bd2a758761dacac6fbf387 (patch) | |
| tree | b795b51d8bcd5b905dc7e42fe9f68ccb2785cd12 /var | |
| parent | 059daa20128808533d241eb9562547bc9c6cd5d1 (diff) | |
| download | spack-5737155dd0de1adc51bd2a758761dacac6fbf387.tar.gz spack-5737155dd0de1adc51bd2a758761dacac6fbf387.tar.bz2 spack-5737155dd0de1adc51bd2a758761dacac6fbf387.tar.xz spack-5737155dd0de1adc51bd2a758761dacac6fbf387.zip | |
trinity: full dependencies (#9064)
Diffstat (limited to 'var')
| -rw-r--r-- | var/spack/repos/builtin/packages/trinity/package.py | 31 |
1 files changed, 31 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/trinity/package.py b/var/spack/repos/builtin/packages/trinity/package.py index 5daad5e02f..635e07290f 100644 --- a/var/spack/repos/builtin/packages/trinity/package.py +++ b/var/spack/repos/builtin/packages/trinity/package.py @@ -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 @@ class Trinity(MakefilePackage): 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) |