sequenceserver 0.7.3 → 0.7.4
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- data/bin/sequenceserver +52 -7
- data/lib/sequenceserver/database_formatter.rb +3 -3
- data/sequenceserver.gemspec +1 -1
- metadata +4 -4
data/bin/sequenceserver
CHANGED
@@ -5,28 +5,73 @@ require 'bundler/setup'
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5
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require 'optparse'
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require 'sequenceserver'
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7
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-
# display name for tools like `ps`
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-
$PROGRAM_NAME = 'sequenceserver'
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-
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8
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# e.g:
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9
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# sequenceserver --config .sequenceserver.conf format_database
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begin
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# parse command line till first non-option, removing parsed options from ARGV
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OptionParser.new do |opts|
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+
opts.banner =<<BANNER
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+
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SUMMARY
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+
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custom, local, BLAST server
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+
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USAGE
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sequenceserver [options] [subcommand] [subcommand's options]
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Example:
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# launch SequenceServer with the given config file
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$ sequenceserver --config ~/.sequenceserver.ants.conf
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# use the bundled database formatter utility to prepare databases for use
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# with SequenceServer
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$ sequenceserver format-databases
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DESCRIPTION
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SequenceServer lets you rapidly set up a BLAST+ server with an intuitive user
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interface for use locally or over the web.
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SUB-COMMANDS
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format-databases:
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prepare BLAST databases for use with SequenceServer
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Run '#{$0} format-databases -h' for help.
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OPTIONS
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BANNER
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opts.on('-c', '--config CONFIG_FILE', 'Use the given configuration file') do |config_file|
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48
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SequenceServer::App.config_file = File.expand_path(config_file)
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end
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end.order!
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# of the remaining items in ARGV, the first one must be a subcommand
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-
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-
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-
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-
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subcommand = ARGV.shift
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+
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if subcommand
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# process subcommands now
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case subcommand
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when 'format-databases'
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require 'sequenceserver/database_formatter'
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exit
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else
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puts "invalid subcommand: #{subcommand}"
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puts "Run '#{$0} -h' for help with command line options."
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exit
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end
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end
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rescue OptionParser::InvalidOption =>e
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puts e
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+
puts "Run '#{$0} -h' for help with command line options."
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exit
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end
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73
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# display name for tools like `ps`
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$PROGRAM_NAME = 'sequenceserver'
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+
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SequenceServer::App.run!
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@@ -152,12 +152,12 @@ SUMMARY
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USAGE
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-
sequenceserver
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+
sequenceserver format-databases [--verbose] [blast_database_directory]
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Example:
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-
$ sequenceserver
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-
$ sequenceserver
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+
$ sequenceserver format-databases ~/db # explicitly specify a database directory
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$ sequenceserver format-databases # use the database directory in config.yml
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DESCRIPTION
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data/sequenceserver.gemspec
CHANGED
metadata
CHANGED
@@ -1,13 +1,13 @@
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1
1
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--- !ruby/object:Gem::Specification
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2
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name: sequenceserver
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3
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version: !ruby/object:Gem::Version
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-
hash:
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4
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+
hash: 11
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5
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prerelease:
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6
6
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segments:
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7
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- 0
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8
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- 7
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9
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-
-
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-
version: 0.7.
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+
- 4
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+
version: 0.7.4
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platform: ruby
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authors:
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- Anurag Priyam
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@@ -17,7 +17,7 @@ autorequire:
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bindir: bin
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cert_chain: []
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-
date: 2011-12-
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+
date: 2011-12-23 00:00:00 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: bundler
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