Hi there,
I setup sequence server interactively in a directory and it worked great. However, when I tried to set sequence server up again, it kept referring to that same directory. Could you add an option to sequence server where it forgets its currently utilized configuration (-reset or something)
Also, in an attempt to get sequence server to use a new directory, I specified a non-existing configuration file, as such:
sequenceserver -c sequenceserver.conf
The interactive setup went fine, but then it ran into the following error:
Error:
undefined method `downcase!’ for nil:NilClass
/home/tfallon/.gem/ruby/1.8/gems/sequenceserver-1.0.2/lib/sequenceserver/database.rb:25:in `initialize’
/home/tfallon/.gem/ruby/1.8/gems/sequenceserver-1.0.2/lib/sequenceserver/database.rb:109:in `new’
/home/tfallon/.gem/ruby/1.8/gems/sequenceserver-1.0.2/lib/sequenceserver/database.rb:109:in `scan_databases_dir’
/home/tfallon/.gem/ruby/1.8/gems/sequenceserver-1.0.2/lib/sequenceserver/database.rb:106:in `each_line’
/home/tfallon/.gem/ruby/1.8/gems/sequenceserver-1.0.2/lib/sequenceserver/database.rb:106:in `scan_databases_dir’
/usr/lib/ruby/1.8/open3.rb:86:in `popen3’
/home/tfallon/.gem/ruby/1.8/gems/sequenceserver-1.0.2/lib/sequenceserver/database.rb:102:in `scan_databases_dir’
/home/tfallon/.gem/ruby/1.8/gems/sequenceserver-1.0.2/lib/sequenceserver.rb:130:in `init_database’
/home/tfallon/.gem/ruby/1.8/gems/sequenceserver-1.0.2/lib/sequenceserver.rb:40:in `init’
/home/tfallon/.gem/ruby/1.8/gems/sequenceserver-1.0.2/bin/sequenceserver:131
/home/tfallon/.gem/ruby/1.8/gems/slop-3.6.0/lib/slop.rb:260:in `call’
/home/tfallon/.gem/ruby/1.8/gems/slop-3.6.0/lib/slop.rb:260:in `parse!’
/home/tfallon/.gem/ruby/1.8/gems/slop-3.6.0/lib/slop.rb:65:in `parse!’
/home/tfallon/.gem/ruby/1.8/gems/sequenceserver-1.0.2/bin/sequenceserver:12
/home/tfallon/.gem/ruby/1.8/bin/sequenceserver:19:in `load’
/home/tfallon/.gem/ruby/1.8/bin/sequenceserver:19
After deleting the blast database files (.nsi etc), and retrying setup, it worked fine and sequence server is fully working.