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资源说明：A flexible bioinformatics search tool.
= Quorum {
}[http://travis-ci.org/ncgr/quorum] {
}[https://gemnasium.com/ncgr/quorum]
A flexible bioinformatics search tool.
Quorum is a Rails 3.1 mountable engine that supports the following
bioinformatics search tools.
* NCBI Blast+ (http://blast.ncbi.nlm.nih.gov)
Dependencies:
* Ruby >= 1.9.2
* Rails >= 3.1.0
* Redis >= 0.900 for Resque (https://github.com/defunkt/resque)
* NCBI Blast+ (ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST)
* Emboss (http://emboss.sourceforge.net)
See the gem in action.
http://medplants.ncgr.org/quorum/jobs/new
== Installation
Use the latest stable Rails release with Quorum.
gem install quorum
After you install Quorum and add it to your Gemfile, run the generator.
rails generate quorum:install
The generator will create a directory in your application's root path
quorum/
as well as the necessary config files to run and customize Quorum. You
MUST customize "config/quorum_settings.yml" before using Quorum. See Remote
Machine Setup below if you choose to execute Quorum remotely.
Migrate the database.
rake quorum:install:migrations
rake db:migrate
== Upgrading?
Follow these steps to safely upgrade Quorum.
* Make a copy of "config/quorum_settings.yml".
cp config/quorum_settings.yml config/quorum_settings.yml.old
* If you overrode Quorum's styles and / or views, make a copy of the
existing directories before upgrading.
cp -R app/assets/stylesheets/quorum app/assets/stylesheets/quorum_old
cp -R app/views/quorum/jobs app/views/quorum/jobs_old
* Run the install generator and answer "Yes" to all conflicts.
rails generate quorum:install
* Copy the old Search Database(s) to the newly generated
"config/quorum_settings.yml" file.
* Update the database migrations.
rake quorum:install:migrations
rake db:migrate
* If applicable, override Quorum's views, styles and images.
* Update the remote machine(s).
== Getting Started
=== NCBI Blast+ Setup
Build your NCBI Blast+ database(s) using the rake task below.
rake quorum:blastdb:build
Arguments:
* DIR= - path to {.tgz, .tar.gz, .tbz, .tar.bz2} files containing raw data.
Separate multiple directories with a colon (:).
DIR=/path/to/dir:/path/to/another/dir
* TYPE= - type of Blast database to build {both, prot, nucl}. Defaults to
both.
* PROT_FILE_NAME= - name of the file containing protein data. Defaults to
peptides.fa.
* NUCL_FILE_NAME= - name of the file containing nucleotide data. Defaults
to contigs.fa.
* REBUILD_DB= - removes existing blast database(s) before building {true or
false}. Defaults to false.
* EMPTY= - skip makeblastdb and create necessary directories {true or false}.
Defaults to false. Set this argument to true if you wish to create your own
Blast database(s).
Example:
rake quorum:blastdb:build DIR=/path/to/dir:/path/to/another/dir TYPE=nucl \
NUCL_FILE_NAME=my_contigs.fa REBUILD_DB=true
Empty example:
rake quorum:blastdb:build EMPTY=true
For a full list of supported arguments.
rake -D
Don't forget to update "config/quorum_settings.yml" with your newly created
database(s).
==== Download Blast Hit Sequence
Quorum provides a link to download a Blast hit sequence in the detailed report.
For this process to work smoothly, the sequence identifier MUST be unique
across ALL Blast databases.
Example:
"example_blast_database/contigs.fa"
>my_unique_sequence_identifier_201201201327077953
ATGC...
"another_example_blast_database/contigs.fa"
>my_unique_sequence_identifier_201201201327078017
CGTA...
If the sequence identifiers are not unique across all Blast databases and
you wish to remove the link to download a Blast hit sequence, follow the
steps below.
* Override Quorum's views (see Customize Quorum below)
* Comment out or remove the lines below in
"app/views/quorum/jobs/templates/_blast_detailed_report_template.html.erb"
=== Remote Machine Setup -- Recommended for Production Use
Follow the steps below to execute Quorum remotely via Net::SSH.
* Ensure your ActiveRecord Database adapter in "config/database.yml" is set to
*any* supported adapter other than sqlite3.
* Ensure your database host is set and accessible via the remote machine(s).
* Ensure you have supplied the necessary information in
"config/quorum_settings.yml" to execute Quorum remotely.
blast:
remote: true
ssh_host: remote.machine.org
ssh_user: remote_user
Net::SSH.start() optional params (http://net-ssh.github.com/ssh/v2/api/index.html)
ssh_options:
password: "secret"
port: 8888
* Tar and compress quorum.
tar -czvf quorum.tar.gz quorum/
* Copy the newly created tarball to the remote machine.
scp quorum.tar.gz @:/path/to/install
* Expand the tarball on the remote machine.
ssh @
tar -xzvf quorum.tar.gz
* Ensure Quorum script dependencies are added to the remote machine's PATH.
If the remote machine doesn't have a .bashrc file, create one.
touch /path/to/.bashrc
and add script dependencies to PATH.
echo "export PATH=/path/to/dependencies:$PATH" >> /path/to/.bashrc
=== Customize Quorum's Views, Styles and Images
To override Quorum's default views, run the generator.
rails generate quorum:views
A copy of Quorum's layouts and views can be found in your application under
"app/views/layouts/quorum/" "app/views/quorum/".
To override Quorum's default styles, run the generator.
rails generate quorum:styles
A copy of Quorum's styles can be found in your application under
"app/assets/stylesheets/quorum/". If your application has existing styles,
it's a good idea to remove
*= require_tree .
in "app/assets/stylesheets/application.css" and require your stylesheets
individually.
To override Quorum's default images, run the generator.
rails generate quorum:images
A copy of Quorum's images can be found in your application under
"app/assets/images/quorum/".
==== jQuery UI
Don't like Quorum's jQuery UI theme? Override it!
* Override Quorum's styles and images.
* Roll your own jQuery UI theme. http://jqueryui.com/themeroller
* Replace Quorum's theme in "app/assets/{stylesheets:images}/quorum" with
your own.
==== Don't plan on supporting all of Quorum's alogrithms?
Override Quorum's views and comment out any unwanted algorithms in
"app/views/quorum/jobs/new.html.erb" and
"app/views/quorum/jobs/show.html.erb".
For example:
Remove Blastp in "app/views/quorum/jobs/new.html.erb"
<%# Search Algorithms %>
<%# Comment out an algorithm below to remove it from the form. %>
<%# blastn %>
<%= render :partial => "quorum/jobs/form/blastn_form", :locals => {
:f => f, :blast_dbs => @blast_dbs } %>
<%# blastx %>
<%= render :partial => "quorum/jobs/form/blastx_form", :locals => {
:f => f, :blast_dbs => @blast_dbs } %>
<%# tblastn %>
<%= render :partial => "quorum/jobs/form/tblastn_form", :locals => {
:f => f, :blast_dbs => @blast_dbs } %>
<%# blastp %>
<% render :partial => "quorum/jobs/form/blastp_form", :locals => {
:f => f, :blast_dbs => @blast_dbs } %>
<%# End Search Algorithms %>
Remove Blastp in "app/views/quorum/jobs/show.html.erb"
<%# Search results per algorithm %>
Blastn
Searching... <%= image_tag "quorum/loading.gif" %>
Blastx
Searching... <%= image_tag "quorum/loading.gif" %>
Tblastn
Searching... <%= image_tag "quorum/loading.gif" %>
==== Don't like Quorum's default show template?
Override Quorum's views and specify your own JavaScript callback function!
See "app/views/quorum/show.html.erb" for more details.
For an example using d3.js (https://github.com/mbostock/d3) see:
https://github.com/ncgr/lis_sequence_search
=== Redis
For detailed Redis installation instructions, follow the links below.
* Redis (http://redis.io)
* Resque (https://github.com/defunkt/resque)
=== Resque
Quorum provides a simple Rails environment rake task for spawning Resque
workers. To customize Resque workers by adding monitoring etc., follow
the link below.
* Resque (https://github.com/defunkt/resque)
==== Resque Web Interface
Quorum mounts Resque's web interface by default via
mount Resque::Server.new, :at => "/quorum/resque"
in "config/routes.rb". The line above is fine for development, however, in
production it's best to grant authenticated users access to "/quorum/resque".
HTTP Basic Example:
"config/initializers/resque_http_auth.rb"
Resque::Server.use(Rack::Auth::Basic) do |user, password|
user == "resque"
password == "secret"
end
Devise Example:
"config/routes.rb"
authenticate :user do
mount Resque::Server.new, :at => "/quorum/resque"
end
Devise plus Declarative Authorization Example:
"config/routes.rb"
# Only superusers can access Resque's web interface.
resque_constraint = lambda do |request|
request.env["warden"].authenticate? &&
request.env["warden"].user.role_symbols.include?(:superuser)
end
constraints resque_constraint do
mount Resque::Server.new, :at => "/quorum/resque"
end
=== I18n
To customize Quorum flash messages, edit "config/locales/quorum.en.yml".
== Additional Information
=== Bugs?
https://github.com/ncgr/quorum/issues
=== Contributing
* Fork Quorum
* Create a topic branch git checkout -b my_branch
* Push to your branch git push origin my_branch
* Create a pull request from your branch
* Find your name added to the README under Contributors
=== TODO
* Add GFF3 annotations to detailed Blast reports
* Add link to download multiple Blast hit sequences in detailed report
* Support Hmmer3
=== Maintained By
* Ken Seal (https://github.com/hunzinker)
=== Contributors
* John Crow (https://github.com/crowja)
* Andrew Farmer (https://github.com/adf-ncgr)
== License
MIT License. Copyright NCGR http://ncgr.org
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