In the demo SequenceServer page at:
The databases are divided into two named groups, Nucleotide Databases and Protein Databases. How can I achieve the same effect?
I have genome, transcriptome, and protein fasta files organized into different subdirectories of the root location specified in .sequenceserver.conf.
When I launched sequence server for the first time, it automatically located and built databases in the first of these subdirectories, but not the other two.
Cheers,
Michael
Hi,
I just tried blasting at https://antgenomes.org/blast/ with a protein sequence and this is what I got (an error):
Errno::ENOENT - No such file or directory - getcwd: /data/home/fourmidable/archive/www/sequenceserver/src/custom/lib/sequenceserver/blast/formatter.rb:44:in `chdir' /data/home/fourmidable/archive/www/sequenceserver/src/custom/lib/sequenceserver/blast/formatter.rb:44:in `run' /data/home/fourmidable/archive/www/sequenceserver/src/custom/lib/sequenceserver/blast/formatter.rb:20:in `initialize' /data/home/fourmidable/archive/www/sequenceserver/src/custom/lib/sequenceserver/blast/report.rb:36:in `new' /data/home/fourmidable/archive/www/sequenceserver/src/custom/lib/sequenceserver/blast/report.rb:36:in `generate' /data/home/fourmidable/archive/www/sequenceserver/src/custom/lib/sequenceserver/blast/report.rb:21:in `initialize' /data/home/fourmidable/archive/www/sequenceserver/src/custom/lib/sequenceserver/blast.rb:97:in `new' /data/home/fourmidable/archive/www/sequenceserver/src/custom/lib/sequenceserver/blast.rb:97:in `run' /data/home/fourmidable/archive/www/sequenceserver/src/custom/lib/sequenceserver/routes.rb:125:in `block in <class:Routes>' /data/home/fourmidable/.gem/ruby/2.2.0/gems/sinatra-1.4.6/lib/sinatra/base.rb:1610:in `call' /data/home/fourmidable/.gem/ruby/2.2.0/gems/sinatra-1.4.6/lib/sinatra/base.rb:1610:in `block in compile!' /data/home/fourmidable/.gem/ruby/2.2.0/gems/sinatra-1.4.6/lib/sinatra/base.rb:974:in `[]' /data/home/fourmidable/.gem/ruby/2.2.0/gems/sinatra-1.4.6/lib/sinatra/base.rb:974:in `block (3 levels) in route!' /data/home/fourmidable/.gem/ruby/2.2.0/gems/sinatra-1.4.6/lib/sinatra/base.rb:993:in `route_eval' /data/home/fourmidable/.gem/ruby/2.2.0/gems/sinatra-1.4.6/lib/sinatra/base.rb:974:in `block (2 levels) in route!' /data/home/fourmidable/.gem/ruby/2.2.0/gems/sinatra-1.4.6/lib/sinatra/base.rb:1014:in `block in process_route' /data/home/fourmidable/.gem/ruby/2.2.0/gems/sinatra-1.4.6/lib/sinatra/base.rb:1012:in `catch' /data/home/fourmidable/.gem/ruby/2.2.0/gems/sinatra-1.4.6/lib/sinatra/base.rb:1012:in `process_route' /data/home/fourmidable/.gem/ruby/2.2.0/gems/sinatra-1.4.6/lib/sinatra/base.rb:972:in `block in route!' /data/home/fourmidable/.gem/ruby/2.2.0/gems/sinatra-1.4.6/lib/sinatra/base.rb:971:in `each' /data/home/fourmidable/.gem/ruby/2.2.0/gems/sinatra-1.4.6/lib/sinatra/base.rb:971:in `route!' /data/home/fourmidable/.gem/ruby/2.2.0/gems/sinatra-1.4.6/lib/sinatra/base.rb:1084:in `block in dispatch!' /data/home/fourmidable/.gem/ruby/2.2.0/gems/sinatra-1.4.6/lib/sinatra/base.rb:1066:in `block in invoke' /data/home/fourmidable/.gem/ruby/2.2.0/gems/sinatra-1.4.6/lib/sinatra/base.rb:1066:in `catch' /data/home/fourmidable/.gem/ruby/2.2.0/gems/sinatra-1.4.6/lib/sinatra/base.rb:1066:in `invoke' /data/home/fourmidable/.gem/ruby/2.2.0/gems/sinatra-1.4.6/lib/sinatra/base.rb:1081:in `dispatch!' /data/home/fourmidable/.gem/ruby/2.2.0/gems/sinatra-1.4.6/lib/sinatra/base.rb:906:in `block in call!' /data/home/fourmidable/.gem/ruby/2.2.0/gems/sinatra-1.4.6/lib/sinatra/base.rb:1066:in `block in invoke' /data/home/fourmidable/.gem/ruby/2.2.0/gems/sinatra-1.4.6/lib/sinatra/base.rb:1066:in `catch' /data/home/fourmidable/.gem/ruby/2.2.0/gems/sinatra-1.4.6/lib/sinatra/base.rb:1066:in `invoke' /data/home/fourmidable/.gem/ruby/2.2.0/gems/sinatra-1.4.6/lib/sinatra/base.rb:906:in `call!' /data/home/fourmidable/.gem/ruby/2.2.0/gems/sinatra-1.4.6/lib/sinatra/base.rb:894:in `call' /data/home/fourmidable/.gem/ruby/2.2.0/gems/rack-1.6.4/lib/rack/head.rb:13:in `call' /data/home/fourmidable/.gem/ruby/2.2.0/gems/sinatra-1.4.6/lib/sinatra/base.rb:181:in `call' /data/home/fourmidable/.gem/ruby/2.2.0/gems/sinatra-1.4.6/lib/sinatra/base.rb:2021:in `call' /data/home/fourmidable/.gem/ruby/2.2.0/gems/sinatra-1.4.6/lib/sinatra/base.rb:1486:in `block in call' /data/home/fourmidable/.gem/ruby/2.2.0/gems/sinatra-1.4.6/lib/sinatra/base.rb:1795:in `synchronize' /data/home/fourmidable/.gem/ruby/2.2.0/gems/sinatra-1.4.6/lib/sinatra/base.rb:1486:in `call' /data/home/fourmidable/archive/www/sequenceserver/src/custom/lib/sequenceserver.rb:95:in `call' /data/home/fourmidable/.gem/ruby/2.2.0/gems/rack-1.6.4/lib/rack/handler/webrick.rb:88:in `service' /opt/rubies/ruby-2.2.0/lib/ruby/2.2.0/webrick/httpserver.rb:138:in `service' /opt/rubies/ruby-2.2.0/lib/ruby/2.2.0/webrick/httpserver.rb:94:in `run' /opt/rubies/ruby-2.2.0/lib/ruby/2.2.0/webrick/server.rb:294:in `block in start_thread'
Cheers,
Lukasz
Hi Michael, Hi Lukasz,
Michael, I have responded to your query on GitHub and will prefer to continue the conversation there if okay with you: https://github.com/wurmlab/sequenceserver/issues/459
Lukasz, thanks for reporting the issue. You should be able run BLAST searches on antgenomes.org/blast now. The issue you reported is a recurring one (due to network constraints), so please don’t hesitate to contact again if you run into it.
Priyam