From 82dbe8398967855b5b97d5a4a55fa4699a23acd3 Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Fri, 28 Sep 2012 03:00:17 +0000 Subject: [PATCH] in progress --- forester/ruby/evoruby/exe/run_phylo_pipeline.rb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/forester/ruby/evoruby/exe/run_phylo_pipeline.rb b/forester/ruby/evoruby/exe/run_phylo_pipeline.rb index 163def7..e4889ff 100755 --- a/forester/ruby/evoruby/exe/run_phylo_pipeline.rb +++ b/forester/ruby/evoruby/exe/run_phylo_pipeline.rb @@ -20,11 +20,10 @@ module Evoruby D2F = "/home/czmasek/SOFTWARE/FORESTER/DEV/forester/forester/ruby/evoruby/exe/d2f.rb" DSX = "/home/czmasek/SOFTWARE/FORESTER/DEV/forester/forester/ruby/evoruby/exe/dsx.rb" - def run unless ARGV.length >= 4 && ARGV.length <= 6 error "arguments are: " + - " [E-value for hmmscan, default is 20] [hmmscan option, default is --nobias]" + " [E-value for hmmscan, default is 20] [hmmscan option, default is --nobias, --max for no heuristics]" end input = ARGV[ 0 ] @@ -54,6 +53,7 @@ module Evoruby base_name = get_base_name input + puts puts "1. hmmscan:" cmd = "#{HMMSCAN} #{hmmscan_option} --domtblout #{base_name}_hmmscan_#{e_for_hmmscan.to_s} -E #{e_for_hmmscan.to_s} #{PFAM}Pfam-A.hmm #{input}" run_command( cmd ) -- 1.7.10.2