From 418db4e9106371976d0ac3d95b4b4bf5adf3ffc8 Mon Sep 17 00:00:00 2001 From: Glenn Johnson Date: Tue, 8 Jun 2021 04:08:10 -0500 Subject: gatk: make r a variant (#24189) 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. --- var/spack/repos/builtin/packages/gatk/package.py | 13 ++++++++++++- 1 file changed, 12 insertions(+), 1 deletion(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/gatk/package.py b/var/spack/repos/builtin/packages/gatk/package.py index f1a0511b70..f83ead3d2d 100644 --- a/var/spack/repos/builtin/packages/gatk/package.py +++ b/var/spack/repos/builtin/packages/gatk/package.py @@ -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) -- cgit v1.2.3-70-g09d2