Hi, there are several pod errors resulting in error messages in man pages. Here is a patch to fix those.
--- a/lib/Genome/Model/Tools/Music/Bmr/CalcCovgHelper.pm +++ b/lib/Genome/Model/Tools/Music/Bmr/CalcCovgHelper.pm @@ -60,7 +60,6 @@ up these base-counts across all ROIs of each gene in the sample, but covered bases that lie within overlapping ROIs are not counted more than once towards these total counts. -=back HELP } @@ -110,6 +109,8 @@ =back +=back + EOS ); } --- a/lib/Genome/Model/Tools/Music/ClinicalCorrelation.pm +++ b/lib/Genome/Model/Tools/Music/ClinicalCorrelation.pm @@ -135,7 +135,7 @@ =item * Columns must be ordered as such: -=item [ analysis_type clinical_data_trait_name variant/gene_name covariates memo ] +=item * [ analysis_type clinical_data_trait_name variant/gene_name covariates memo ] =item * The 'analysis_type' column must contain either "Q", indicating a quantative trait, or "B", indicating a binary trait will be examined. --- a/lib/Genome/Model/Tools/Music/PathScan.pm +++ b/lib/Genome/Model/Tools/Music/PathScan.pm @@ -116,6 +116,7 @@ =back =back + EOS ); } --- a/lib/Genome/Model/Tools/Music/Smg.pm +++ b/lib/Genome/Model/Tools/Music/Smg.pm @@ -83,6 +83,7 @@ =back =back + EOS ); } --- a/lib/Genome/Model/Tools/Music/Bmr/CalcCovg.pm +++ b/lib/Genome/Model/Tools/Music/Bmr/CalcCovg.pm @@ -83,6 +83,7 @@ cmd-list-file and cmd-prefix arguments or you will just be re-creating a list of commands. =back + HELP }