selfishly add Ben's name to the author list
gracefully deal with short BLAST query strings that are not classified as either protein or nucleotide, instead of throwing a whiny nil error. #issuenbr 36
README: expand 'current contributors' section
README: expand Yannick's byline

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README: replace references to fourmidable with antgenomes.org

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add citation

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README: transferred FAQ from wiki to README

because it is confusing to have an empty wiki page

Signed-off-by: Yannick Wurm <yannick.wurm@unil.ch>
Bugfix with blastdbcmd in BLAST 2.2.22
---

* blastdbcmd sometimes outputs an empty line, which led to a crash
  see: https://github.com/yannickwurm/sequenceserver/issues/50
  Fixed.

Signed-off-by: Yannick Wurm <yannick.wurm@unil.ch>
sequencehelpers: use the path to blast binaries from config.yml (fix #40)

Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
app: move out validation of advanced parameters to a separate method

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Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
blast: introduce functions to blast to a BLAST Archive

BLAST Archive format, introduced in BLAST+ 2.2.24, can later be
reformatted with the blast_formatter tool. This offers more flexibility
than directly blasting to text or html.

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Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
app: Blasting to HTML output now occurs via a blast archive

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Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
app: visually separate the results of a multi-query blast (#10)

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Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
maint: clean up whitespace issues in search.erb

While the rest of the project uses only spaces for indentation and
alignment, search.erb (for historical reasons) used only tabs. Unless
specifically taken care, editing search.erb would produce ugly diffs due
to mixing up of tabs and spaces. Changed search.erb to be space only.

Fixed minor indentation hiccups carried over from previous edits.

Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
cleanup: do not load JS for error page 500

Loading JS for error pages is unwarranted.

Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
deploy: fix suburi deployment quirks (fix #49)

Rack [specifies][1] `SCRIPT_NAME` environment variable be set and
available to apps to be able to determine their virtual location.
Sinatra's URL helper, `Sinatra::Base#url`, takes `SCRIPT_NAME` (and
other parameters) into account for URL construction. Lets use it to
guard against broken URLs when deploying SequenceServer to a sub URI.

Note:

* I am not sure how to, or if it even makes sense to use the url helper
  in search.js. As a workaround, the AJAX request is fired to the
  current URL. This works because:

    1. only the main page loads and uses search.js

    2. the same route that renders the main page and handles BLAST
       queries, is responsible for AJAX request too (the same route
       behaves differently for different types of requests).

* The deployment scheme needs to ensure that `SCRIPT_NAME` environment
  variable is set. I didn't have to set it on both of my Phusion
  Passenger based test beds.

[1]: http://rack.rubyforge.org/doc/files/SPEC.html

Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
Clarified usage terms

-- Signed off by Yannick Wurm
ui: add a helper method to check checkboxes and radiobuttons

Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
ui: automatically select the only possible database (close #45)

possible database => non-disabled entries in the database list. Nothing
supremely intelligent, eh?

Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
config: make the example BLAST+ directory 2.2.25+

To be in line with recommended BLAST+ version.

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Signed-off-by: Ben J Woodcroft <gmail.com after donttrustben>
Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>