sequenceserver 0.7.3 → 0.7.4

data/bin/sequenceserver

@@ -5,28 +5,73 @@ require 'bundler/setup'
 require 'optparse'
 require 'sequenceserver'
 
-# display name for tools like `ps`
-$PROGRAM_NAME = 'sequenceserver'
-
 # e.g:
 # sequenceserver --config .sequenceserver.conf format_database
 begin
   # parse command line till first non-option, removing parsed options from ARGV
   OptionParser.new do |opts|
+    opts.banner =<<BANNER
+
+SUMMARY
+
+  custom, local, BLAST server
+
+USAGE
+
+  sequenceserver [options] [subcommand] [subcommand's options]
+
+  Example:
+
+    # launch SequenceServer with the given config file
+    $ sequenceserver --config ~/.sequenceserver.ants.conf
+
+    # use the bundled database formatter utility to prepare databases for use
+    # with SequenceServer
+    $ sequenceserver format-databases
+
+DESCRIPTION
+
+  SequenceServer lets you rapidly set up a BLAST+ server with an intuitive user
+  interface for use locally or over the web.
+
+SUB-COMMANDS
+
+  format-databases:
+    prepare BLAST databases for use with SequenceServer
+
+    Run '#{$0} format-databases -h' for help.
+
+OPTIONS
+
+BANNER
     opts.on('-c', '--config CONFIG_FILE', 'Use the given configuration file') do |config_file|
       SequenceServer::App.config_file = File.expand_path(config_file)
     end
   end.order!
 
   # of the remaining items in ARGV, the first one must be a subcommand
-  case ARGV.shift
-  when 'format_database'
-    require 'sequenceserver/database_formatter'
-    exit
+  subcommand = ARGV.shift
+
+  if subcommand
+    # process subcommands now
+
+    case subcommand
+    when 'format-databases'
+      require 'sequenceserver/database_formatter'
+      exit
+    else
+      puts "invalid subcommand: #{subcommand}"
+      puts "Run '#{$0} -h' for help with command line options."
+      exit
+    end
   end
 rescue OptionParser::InvalidOption =>e
   puts e
+  puts "Run '#{$0} -h' for help with command line options."
   exit
 end
 
+# display name for tools like `ps`
+$PROGRAM_NAME = 'sequenceserver'
+
 SequenceServer::App.run!

data/lib/sequenceserver/database_formatter.rb

@@ -152,12 +152,12 @@ SUMMARY
 
 USAGE
 
-  sequenceserver format_database [--verbose] [blast_database_directory]
+  sequenceserver format-databases [--verbose] [blast_database_directory]
 
   Example:
 
-    $ sequenceserver format_database ~/db  # explicitly specify a database directory
-    $ sequenceserver format_database       # use the database directory in config.yml
+    $ sequenceserver format-databases ~/db  # explicitly specify a database directory
+    $ sequenceserver format-databases      # use the database directory in config.yml
 
 DESCRIPTION
 

data/sequenceserver.gemspec

@@ -1,7 +1,7 @@
 Gem::Specification.new do |s|
   # meta
   s.name        = 'sequenceserver'
-  s.version     = '0.7.3'
+  s.version     = '0.7.4'
   s.authors     = ['Anurag Priyam', 'Ben J Woodcroft', 'Yannick Wurm']
   s.email       = 'anurag08priyam@gmail.com'
   s.homepage    = 'http://sequenceserver.com'

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: sequenceserver
 version: !ruby/object:Gem::Version 
-  hash: 5
+  hash: 11
   prerelease: 
   segments: 
   - 0
   - 7
-  - 3
-  version: 0.7.3
+  - 4
+  version: 0.7.4
 platform: ruby
 authors: 
 - Anurag Priyam
@@ -17,7 +17,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-12-18 00:00:00 Z
+date: 2011-12-23 00:00:00 Z
 dependencies: 
 - !ruby/object:Gem::Dependency 
   name: bundler