Don't fail if R is not installed

[paidi]

Feature request

Tool(s) involved

Subcommands: CollectInsertSizeMetrics, QualityScoreDistribution, MeanQualityByCycle, CollectBaseDistributionByCycle, CollectGcBiasMetrics, CollectRnaSeqMetrics, CollectRrbsMetrics, CollectMultipleMetrics, CollectWgsMetricsWithNonZeroCoverage (and possibly more)

Description

#1613 introduced a feature where Picard would fail automatically if R was not present, in cases where R is required to generate a plot in a tool. The motivation for this is so that Picard would not run for hours before failing. However, in some applications a user may want to run a tool to generate a metrics file which will be consumed by a downstream tool (such as https://github.com/ewels/MultiQC) and not need the PDF chart. In these cases, it would be useful to be able to run Picard on machines without an R installation and skipping the plot generation when this was the case.

Version

This was using the version of Picard bundled with GATK version 4.2.0.0

[matthdsm]

xref #1720