Itoshi NIKAIDO edited this page Feb 16, 2014 · 10 revisions

Bioconductor Code Search for Package Developers

Full text search system for all of bioconductor devel (2.14) source code on the web. The beta version of the system is opened to public at http://search.bioconductor.JP.

Functions

  • Fast full text search
  • Code highlighting
  • Facet search by package name
  • "More Like this"

Requirement

See Gemfile.

Setup

# Only first time
cd search
bunlde install

# Extract source code from Bioc package and insert database
cd ../make_db
rake load

# Starting solr server
cd ../search
bundle exec rake sunspot:solr:stop
bundle exec rake sunspot:solr:start

# Re-indexing solr, if you need it.
rake sunspot:reindex

# Restarting Rails with passenger, if you need it.
touch tmp/restart.txt

Update database

1. Mirroring bioc-devel

rsync -zrtlv --delete master.bioconductor.org::2.14 /mirror/packages/2.14  > /mirror/update.2.14.txt  2>&1

2. Configure load.rb

emacs -nw /search.bioconductor.jp/make_db/load.rb
base_dir = '/mirror/packages/2.14/bioc/src/contrib'

3. Load database

rake load
rake sunspot:reindex
touch tmp/restart.txt

License

Source codes of this system (without sources of each bioconductor package) are licensed under a Artistic-2.0.

Itoshi NIKAIDO dritoshi@gmail.com Copyright (C) 2012-2014. Itoshi NIKAIDO.

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