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gatk: make r a variant (#24189)

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According to the docs, r is needed for plotting, but plotting is
untested. In addition, the specific version requirement of java for gatk
could lead to multiple installations of r being triggered in an
environment. That might cause people to have to be deliberate about
java in a deployment. All in all, it seems that r is better as a
variant for gatk.
This commit is contained in:
Glenn Johnson 2021-06-08 04:08:10 -05:00 committed by GitHub
parent f231ae97f4
commit 418db4e910
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1 changed files with 12 additions and 1 deletions
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var/spack/repos/builtin/packages/gatk/package.py
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@ -89,9 +89,20 @@ class Gatk(Package):
url="https://storage.googleapis.com/gatk-software/package-archive/gatk/GenomeAnalysisTK-3.8-0-ge9d806836.tar.bz2"
)
# Make r a variant. According to the gatk docs it is not essential and not
# tested.
# https://github.com/broadinstitute/gatk#R
# Using R to generate plots
# Certain GATK tools may optionally generate plots using the R installation
# provided within the conda environment. If you are uninterested in plotting,
# R is still required by several of the unit tests. Plotting is currently
# untested and should be viewed as a convenience rather than a primary
# output.
variant('r', default=False, description='Use R for plotting')
depends_on("java@8", type="run")
depends_on("python@2.6:2.8,3.6:", type="run", when="@4.0:")
depends_on("r@3.2:", type="run", when="@4.0:")
depends_on("r@3.2:", type="run", when="@4.0: +r")
def install(self, spec, prefix):
mkdirp(prefix.bin)