Commit 983caf64 authored by Holger Brandl's avatar Holger Brandl

added check for samtools

parent 76f6fe30
......@@ -52,6 +52,7 @@ println("validating system requirements...")
// make sure that STAR is in the PATH
if (evalBash("which STAR").exitCode != 0) throw IllegalArgumentException("STAR aligner is not in PATH")
if (evalBash("which samtools").exitCode != 0) throw IllegalArgumentException("samtools are not in PATH")
System.getenv("NGS_TOOLS").let {
require(it.isNotBlank() && File(it).isDirectory) { "NGS_TOOLS is not defined but needed to locate star_qc.R" }
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