…server * Change default server to EBI Dbfetch server. * The BioRuby BioFetch server is removed. When "-r" option (force to use BioRuby server) is specified, warning message is shown, and the program exits with code 1 (abnormal exit). * Usage message is also changed.
… issue * In lib/bio/io/flatfile/indexer.rb and lib/bio/io/flatfile/index.rb, to fix a bug that invalid index is generated when LANG=en_US.UTF-8, when executing "/usr/bin/sort" (or sort program given by user), doing "/usr/bin/env LC_ALL=C" by default to avoid effects of locales. Note that users can specify path of env program and arguments with options. * In bin/br_bioflat.rb, added new option --env=/path/to/env and --env-arg=XXX (e.g. LC_ALL=C), corresponding to above changes. In addition, fixed a bug --format=XXX option was ignored.
attempts to integrate Rails in shell (but now it is supported by shell/irb.rb and shell/web.rb)
…rs' to avoid modification of bin/* files by RubyGems)
load_session/save_session respectively to avoid method name collision with Kernel#load
…rectory will be used to save session
…iscussion with Tanka-san (.bioruby/script.rb will use this) * access.rb plugin is moved under the plugin directory as a entry.rb * Core is changed to Ghost :)
@config and @cache which are initialized in Bio::Shell.setup as a Hash and have accessors (Bio::Shell.config, Bio::Shell.cache).
…nged to use Bio::Shell::Core::Config & Cache, which have accessor methods like Bio::Shell.config(param, value), Bio::Shell.cache(param, value))
* $bioruby_cache variable is introduced for non persistent configuration
produces MEDLINE abstract in RD format (part of the Ruby's documentation format).