Merge pull request #390 from ASLeonard/optionally_missing_tools

only fail if non-installed programs are required
pangenome · Apr 10, 2024 · de71ee5 · de71ee5
2 parents 0dfa42b + c23e223
commit de71ee5
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diff --git a/partition-before-pggb b/partition-before-pggb
@@ -276,11 +276,15 @@ check_tool_availability "seqwish" "seqwish"
 check_tool_availability "smoothxg" "smoothxg"
 check_tool_availability "odgi" "odgi"
 check_tool_availability "gfaffix" "gfaffix"
+if [ "$vcf_spec" != "false" ]; then
 check_tool_availability "vg" "vg"
 check_tool_availability "vcfbub" "vcfbub"
 check_tool_availability "vcfwave" "vcfwave"
 check_tool_availability "bcftools" "bcftools"
+fi
+if [[ $multiqc == true ]]; then
 check_tool_availability "MultiQC" "multiqc"
+fi
 
 # If there are missing tools, report them and exit
 if [ ${#missing_tools[@]} -ne 0 ]; then

diff --git a/pggb b/pggb
@@ -276,11 +276,15 @@ check_tool_availability "seqwish" "seqwish"
 check_tool_availability "smoothxg" "smoothxg"
 check_tool_availability "odgi" "odgi"
 check_tool_availability "gfaffix" "gfaffix"
+if [ "$vcf_spec" != "false" ]; then
 check_tool_availability "vg" "vg"
 check_tool_availability "vcfbub" "vcfbub"
 check_tool_availability "vcfwave" "vcfwave"
 check_tool_availability "bcftools" "bcftools"
+fi
+if [[ $multiqc == true ]]; then
 check_tool_availability "MultiQC" "multiqc"
+fi
 
 # If there are missing tools, report them and exit
 if [ ${#missing_tools[@]} -ne 0 ]; then