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All documentation now at sequenceserver.com

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Signed-off-by: Yannick Wurm <yannick.wurm@unil.ch>
Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
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-# SequenceServer (Beta 1)
-
-Biologists constantly generate new sequence data. However, it is challenging to effectively
-share and search and compare sequence data. Deploying complex solutions such as
-[GMOD][5] is often overkill, and publicly available front ends for BLAST such as
-[NCBI's wwwblast][21] are difficult to use or install.
-There is a need for an easy-to-deploy and easy-to-use solution.
-
-SequenceServer allows rapid creation of a web page to [BLAST][1] search
-sequence databases by using an intuitive user interface. SequenceServer can
-be used as a local point and click interface to [NCBI BLAST+][2], or to
-provide one over the web. SequenceServer uses [NCBI BLAST+][2],
-[Sinatra][3], and [jQuery][4].
-
-## Features
-
-Ease of use for biologists:
-
-* a single iPod-like search page
-* intuitive and helpful web interface: automatic sequence type detection that helps
- choose appropriate BLAST method and database types
-* links to easily download sequences of BLAST hits
-* support for advanced options.
-
-
-Rapid deployment for bioinformatics administrators:
-
-* assisted formatting of BLAST databases (with sequence type detection)
-* automatic discovery of formatted BLAST databases during startup
-* uses ruby's internal web server (on any open port) or Apache
-* add custom hyperlinks to identified hits (to your genome browser or custom database)
-* open source & freely available for non-profits.
-
-
-## Setup
-
-### Requirements
-
-The following software is required to run SequenceServer:
-
-* [NCBI BLAST+][2] ( at least 2.2.18 )
-* [Ruby][6] ( tested with 1.8.7 and 1.9.2)
-
-### Download
-
-Get the latest version SequenceServer from: https://github.com/yannickwurm/sequenceserver/archives/master.
-
-Or download the zip in the command-line:
-
- wget http://github.com/yannickwurm/sequenceserver/zipball/master -O sequenceserver.zip
-
-
-### Installation
-
-Unzip/Untar the downloaded file, cd to SequenceServer's directory and issue the following command that will make sure you have the required ruby dependencies:
-
- gem install bundler && bundle install
-
-### Either set up BLAST databases from a directory of FASTA sequence files
-
- ruby database_formatter.rb directory_with_fasta_files
-
-The `database_formatter.rb` script will assist you by:
-
- * finding FASTA files in `directory_with_fasta_files` (and in subdirectories too)
- * detecting the sequence type of each file
- * asking you to name each database
- * subsequently running the appropriate `makeblastdb` commands.
-
-### Or set up BLAST databases from a single FASTA sequence file
-In the directory containing the FASTA file, run:
-
- makeblastdb -dbtype <db type> -title <db title> -in <db> -parse_seqids
-
-Where,
-
-* `<db type>` is either `prot`, or `nucl` depending on the type of sequence
-* `<db title>` is what users will see
-* `<db>` is the path to the FASTA file
-* `-parse_seqids` is required to generate links for downloading search
- hits (yes, it's slow on large files).
-* Additional options at `makeblastdb -help`.
-
-
-### Configuration
-
-SequenceServer needs to know the location of the BLAST+ binaries, and the
-BLAST database. This is accomplished by providing a `config.yml` in the
-installation directory.
-
- # .config.yml
- bin: ~/ncbi-blast-2.2.25+/bin/
- database: /Users/me/blast_databases/
-
-A fully commented `example.config.yml` is provided for a start - copy it to
-`config.yml`, uncomment the relevant lines (ie remove the '#' signs),
-edit the values, and run SequenceServer.
-
-
-
-## Running SequenceServer
-
-From the installation directory, run:
-
- ruby sequenceserver.rb
-
-
-SequenceServer will be accessible on port 4567 at http://localhost:4567/ .
-Change the port by editing `config.yml` or with the -p command line option, eg: `ruby sequenceserver.rb -p 8181`.
-
-SequenceServer automatically uses ruby's internal web servers. No need for Apache.
-By default it uses [Webrick][7]. Installling [Thin][8] (`gem install thin`), or [Mongrel][9] (`gem install mongrel`)
-can improve performance.
-
-## Frequently Asked Questions (FAQ)
-
-### Why doesn't sequence retrieval work?
-
-Probably because you forgot the `-parse_seqids` argument when runnidn `makeblastdb` (or they were formatted using legacy `formatdb`). Blast+ 2.2.24 and later indicate that when `-parse_seqids` was not used by leaving a space between `>` and hit identifiers (eg: `> db_sequence001` instead of `>db_sequence001`).
-
-
-### How can I add custom links to hits?
-
-Easy. Edit the `customisation.rb` file and read the examples it provides. To add a single link, uncomment and edit the `construct_custom_sequence_hyperlink` method; to add multiple links edit the `construct_custom_sequence_hyperlinking_line` method.
-
-
-### Can I integrate SequenceServer into an Apache or Nginix server?
-
-Yes. This requires the `passenger` gem. [Details][29].
-
-
-## Who uses SequenceServer?
-
-* 'Beta 1' is deployed by the [Keller lab][10] at [University of
-Lausanne][11]; see [Fourmidable Sequences][12].
-* [Guy Leonard @ National History Museum London][13]
-* Steffen Lemke @ Center for Organismal Studies, Heidelberg.
-* Researchers at [Benaroya Research Institute at Virginia Mason][22]
-* you...
-
-## Reference
-
-A manuscript describing SequenceServer is *in prep*. In the mean time,
-please cite "Priyam A., Woodcroft B.J., Wurm Y *in prep*. **Sequenceserver: BLAST searching made easy**").
-
-
-## Development
-
-SequenceServer is in 'Beta 1'; many exciting features are planned for future release.
-
-Our [issues tracker][13] logs development activities. [feature][14] indicates what is in the pipeline, and [bugs][15] indicates upcoming fixes. Feel free to add comments, vote, report bugs or request features. All contributions, patches and pulls are welcome.
-
-Current contributors:
-
- * [Yannick Wurm][16] is an evolutionary biologist using genomics tools to study the evolution of ant
- societies (eg: [antgenomes.org][23], [fire ant genome][24], [competing fire ant queens][25]). He will be at
- [Queen Mary University London][26] from January 2012.
- * [Anurag Priyam][17]
- * [Cedric Wurm][18]
- * [Ben J Woodcroft][19] is a PhD student in [Melbourne][28] studying protein trafficking in apicomplexan parasites including malaria
- (e.g. [ApiLoc][27]), as well as maintaining a general interest in protein and genome evolution.
- From January 2012 he will be in Queensland.
-
-
-[1]: http://blast.ncbi.nlm.nih.gov/Blast.cgi
-[2]: http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download
-[3]: http://www.sinatrarb.com/
-[4]: http://jquery.com/
-[5]: http://www.gmod.org
-[6]: http://www.ruby-lang.org/en/
-[7]: http://www.ruby-doc.org/stdlib/libdoc/webrick/rdoc/index.html
-[8]: http://code.macournoyer.com/thin/
-[9]: http://rubygems.org/gems/mongrel
-[10]: http://www.antgenomes.org/
-[11]: http://www.unil.ch/central
-[12]: http://www.antgenomes.org/blast
-[13]: https://github.com/yannickwurm/sequenceserver/issues
-[14]: https://github.com/yannickwurm/sequenceserver/issues?labels=feature
-[15]: https://github.com/yannickwurm/sequenceserver/issues?labels=bug
-[16]: http://yannick.poulet.org
-[17]: http://about.me/yeban
-[18]: http://ceddo.gammosaur.com
-[19]: https://github.com/wwood
-[20]: http://gna-phylo.nhm.ac.uk/blast.html
-[21]: http://www.ncbi.nlm.nih.gov/BLAST/docs/wwwblast.html]
-[22]: http://www.benaroyaresearch.org
-[23]: http://yannick.poulet.org/publications/wurm2009antDatabase.pdf
-[24]: http://yannick.poulet.org/publications/wurm2011fireAntGenome.pdf
-[25]: http://www.antgenomes.org/publications/wurm2010fireAntQueenDealationExpression.pdf
-[26]: http://www.sbcs.qmul.ac.uk/
-[27]: http://apiloc.bio21.unimelb.edu.au
-[28]: http://www.biochemistry.unimelb.edu.au/research/res_ralph.html
-[29]: https://github.com/yannickwurm/sequenceserver/wiki/Deploying-SequenceServer-in-Apache-or-Nginix-with-Phusion-Passenger
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+Thanks for downloading SequenceServer!
+
+Documentation available at http://www.sequenceserver.com
+
+-- Yannick Wurm, Ben Woodcroft, Anurag Priyam

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