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sanger-pathogens / Roary

Rapid large-scale prokaryote pan genome analysis
http://sanger-pathogens.github.io/Roary
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cd-hit version not being recognised #529

Open sharbie88 opened 3 years ago

sharbie88 commented 3 years ago

I've just installed Roary v 3.13.0 via conda and running roary -a I get a message

2021/04/08 16:21:25 Determined cd-hit version is Use of uninitialized value in numeric lt (<) at /home/sharb/miniconda3/envs/roary_env/lib/site_perl/5.26.2/Bio/Roary/External/CheckTools.pm line 132.

cd-hit is v 4.8.1.

I've gone through CheckTools.pm and issues #480 and #503 and my script is correct (lines 82-93):

my %cdhit_tools = ( 'cdhit' => { GETVER => "cdhit -h | grep 'CD-HIT version'", REGEXP => qr/version\s+($BIDEC)/i, MINVER => "4.6", }, 'cd-hit' => { GETVER => "cd-hit -h | grep 'CD-HIT version'", REGEXP => qr/version\s+($BIDEC)i/, MINVER => "4.6", } );