sequenceserver 0.6.9 → 0.7.1

data/bin/sequenceserver

@@ -2,9 +2,31 @@
 
 require 'rubygems'
 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.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
+  end
+rescue OptionParser::InvalidOption =>e
+  puts e
+  exit
+end
+
 SequenceServer::App.run!

data/{bin/database_formatter → lib/sequenceserver/database_formatter.rb}

@@ -1,9 +1,10 @@
-#!/usr/bin/env ruby
 # copyright yannick . wurm at unil . ch
 # Finds files, reads first char. if its '>', read 500 lines. Guess sequence type, ask user for title to format as blast database.
 
-require 'rubygems'
-require 'bundler/setup'
+# TODO: bring it under SequenceServer namespace
+# TODO: move the file to a 'command/' sub-directory (probably makes more sense if we have several subcommands)
+# TODO: needs more love (read refactoring) overall
+
 require 'ptools' # for File.binary?(file)
 require 'find'
 require 'logger'
@@ -144,36 +145,32 @@ end
 
 OptionParser.new do |opts|
   opts.banner =<<BANNER
-NAME
 
-  database_formatter.rb - prepare BLAST databases for SequenceServer
+SUMMARY
+
+  prepare BLAST databases for SequenceServer
 
-SYNOPSIS
+USAGE
 
-  ./database_formatter.rb [--verbose] [blast_database_directory]
+  sequenceserver format_database [--verbose] [blast_database_directory]
 
   Example:
 
-    $ ./database_formatter.rb ~/db   # explicitly specify a database directory
-    $ ./database_formatter           # use the database directory in config.yml
+    $ sequenceserver format_database ~/db  # explicitly specify a database directory
+    $ sequenceserver format_database       # use the database directory in config.yml
 
 DESCRIPTION
 
-  database_formatter recursively scans the given 'blast_database_directory' for
-  BLAST databases and formats them for use with SequenceServer.
+  Recursively scan the given 'blast_database_directory' for BLAST databases and
+  formats them for use with SequenceServer.
 
   It automagically detects the database type, and ignores non-db files and
   pre-formatted databases. The 'parse_seqids' makeblastdb options is used.
 
   'blast_database_directory' can be passed as a command line parameter or
-  through config.yml by setting the 'database' key (the same option used by
-  SequenceServer). See example.config.yml. database_formatter will check
-  config.yml only if the command line parameter is missing.
-
-  Failing both, database_formatter will look for 'database' directory relative
-  to the current working directory i.e ./database.
-
-  database_formatter can be used standalone too.
+  through a configuration file by setting the 'database' key (the same option
+  used by SequenceServer). Configuration file will be checked only if the
+  command line parameter is missing.
 
 OPTIONS
 

data/sequenceserver.gemspec

@@ -1,7 +1,7 @@
 Gem::Specification.new do |s|
   # meta
   s.name        = 'sequenceserver'
-  s.version     = '0.6.9'
+  s.version     = '0.7.1'
   s.authors     = ['Anurag Priyam', 'Ben J Woodcroft', 'Yannick Wurm']
   s.email       = 'anurag08priyam@gmail.com'
   s.homepage    = 'http://sequenceserver.com'
@@ -22,7 +22,7 @@ DESC
   s.files         = s.files + ['config.ru',   'example.config.yml']
   s.files         = s.files + ['LICENSE.txt', 'README.txt']
   s.files         = s.files + ['Gemfile',     'sequenceserver.gemspec']
-  s.executables   = ['sequenceserver', 'database_formatter']
+  s.executables   = ['sequenceserver']
   s.require_paths = ['lib']
 
   # post install information

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: sequenceserver
 version: !ruby/object:Gem::Version 
-  hash: 21
+  hash: 1
   prerelease: 
   segments: 
   - 0
-  - 6
-  - 9
-  version: 0.6.9
+  - 7
+  - 1
+  version: 0.7.1
 platform: ruby
 authors: 
 - Anurag Priyam
@@ -69,13 +69,13 @@ description: |
 email: anurag08priyam@gmail.com
 executables: 
 - sequenceserver
-- database_formatter
 extensions: []
 
 extra_rdoc_files: []
 
 files: 
 - lib/sequenceserver.rb
+- lib/sequenceserver/database_formatter.rb
 - lib/sequenceserver/sequencehelpers.rb
 - lib/sequenceserver/customisation.rb
 - lib/sequenceserver/helpers.rb
@@ -107,7 +107,6 @@ files:
 - Gemfile
 - sequenceserver.gemspec
 - bin/sequenceserver
-- bin/database_formatter
 homepage: http://sequenceserver.com
 licenses: 
 - SequenceServer (custom)