initial github.io support

Gemfile

@@ -1,13 +1,13 @@
 source 'http://rubygems.org'
 
-gem 'bio', '~> 1.5', '>= 1.5.0'
-gem 'deep_merge', '~> 1.0', '>= 1.0.1'
-gem 'configatron', '~> 4.5', '>= 4.5.0'
+gem 'bio', '~> 1.5', '= 1.5.0'
+gem 'deep_merge', '~> 1.0', '= 1.0.1'
+gem 'configatron', '~> 4.5', '= 4.5.0'
 
-gem 'orf_finder', '~> 0.1', '>= 0.1.8'
+gem 'orf_finder', '~> 0.1', '= 0.1.8'
 
 group :development do
-  gem 'byebug', '~> 8.2', '>= 8.2.1'
+  gem 'byebug', '~> 8.2', '= 8.2.5'
 end
 
 gem 'rake'

README.md

@@ -3,6 +3,8 @@ MassBLAST
 
 Library to query multiple files against many databases
 
+**We recommend using a packaged release of MassBlast available [at this link](https://github.com/averissimo/mass-blast/releases)**. The only requirement is to have BLAST+ installed. See all the information in the section below.
+
 # Install and usage (from a release)
 
 Pre-packaged releases of MassBlast are available at github, [download here](https://github.com/averissimo/mass-blast/releases) and support:
@@ -15,7 +17,7 @@ Requirements:
   -  [link to download latest version](https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download)
     - note for Windows users:
       1. Can only install 32-bit version of BLSAT+ (latest win32 version is 2.2.30 that can be [downloaded here](ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/))
-      2. If it gives an error, please delete ncbi.ini located at a subdirectory at the AppData folder, if problem persists, submit an issue.
+      2. If it gives an error, please delete `ncbi.ini` located at a subdirectory at the `AppData` folder, if problem persists, submit an issue.
 
 Default options can be changed at user.yml, check user.yml.example for more information (manual soon).
 
@@ -29,6 +31,8 @@ Default options can be changed at user.yml, check user.yml.example for more info
 
 # Install and usage (from source code)
 
+We do not recommend installing from source unless you plan to develop MassBlast further. The package available already has all dependencies pre-packaged and is ready to be used.
+
 Requirements:
 - Ruby interpreter
 - Bundler gem
@@ -89,11 +93,11 @@ Using makeblastdb command that comes bundled with Blast+
 - Navigate to directory
 - Go to directory that has the fasta file with the assembly
 - Run makeblastdb command in that directory
-  
+
   - nucleotides database
 
     $ makeblastdb -in <filename> -dbtype nucl -out "<blast_db_new_name>" -title "<blast_db_new_name>"
-  
+
   - protein database
 
     $ makeblastdb -in <filename> -dbtype nucl -out "<blast_db_new_name>" -title "<blast_db_new_name>"

docs/index.md

@@ -0,0 +1,129 @@
+MassBLAST
+==========
+
+Library to query multiple files against many databases
+
+**We recommend using a packaged release of MassBlast available [at this link](https://github.com/averissimo/mass-blast/releases)**. The only requirement is to have BLAST+ installed. See all the information in the section below.
+
+# Install and usage (from a release)
+
+Pre-packaged releases of MassBlast are available at github, [download here](https://github.com/averissimo/mass-blast/releases) and support:
+  - Linux 32/64-bit
+  - Mac OSX (recent versions)
+  - Windowns (the binaries are 32-bits, due to our packaging tool that includes ruby and other dependencies)
+
+Requirements:
+- BLAST+ installed
+  -  [link to download latest version](https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download)
+    - note for Windows users:
+      1. Can only install 32-bit version of BLSAT+ (latest win32 version is 2.2.30 that can be [downloaded here](ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/))
+      2. If it gives an error, please delete `ncbi.ini` located at a subdirectory at the `AppData` folder, if problem persists, submit an issue.
+
+Default options can be changed at user.yml, check user.yml.example for more information (manual soon).
+
+## How to use it?
+
+- Place fasta files with queries at `db_and_queries/queries` folder.
+- Place blast databases at `db_and_queries/db` folder.
+  - Check "How to setup a Blast database for a transcriptome" below for more information on creating a Blast database.
+- Edit user.yml file to change options and BLAST engine to be used.
+- run mass-blast script (either double click it on Windows or as a command in the command line.
+
+# Install and usage (from source code)
+
+We do not recommend installing from source unless you plan to develop MassBlast further. The package available already has all dependencies pre-packaged and is ready to be used.
+
+Requirements:
+- Ruby interpreter
+- Bundler gem
+- rub `bundle install` at root directory
+- Options are configurable via `config/user.yml` file
+  - Change 'db_parent' and 'query_parent' to specify the parent directories for blast databases and queries
+  - Change 'dbs' and 'folder_queries' to specify the databases that should be used and which query folders should be crawled
+
+  $ ruby script.rb
+
+## External data
+
+The test blast database and the taxonomy database are not kept in the git tree anymore, to get this auxiliary data run the command below or call mass-blast via script.rb
+
+    $ rake bootstrap.rb
+
+If you need to include it on your code use:
+
+    require_relative 'src/download'
+
+    ExternalData.download(path_to_db_parent)
+
+## How to test it
+
+    $  rake spec
+
+## Type of blast implemented
+
+- Blastn
+- TBlastn
+- TBlastx
+
+## Methods available
+
+All different types have two implemented methods, blast and blast_folders
+
+- blast(qfile, db, out_file, query_parent=nil, db_parent=nil)
+  - *qfile*: query file path - string
+  - *db*: database name - string
+  - *out_file*: output file path (can be relative) -string
+  - *query_parent*: parent directory of query (optional) - string
+  - *db_parent*: parent directory of database (optional) - string
+
+*notes:* '*qfile*' and '*db*' arguments can be relative to '*query_parent*' and '*db_parent*' (respectively).
+
+- blast_folders( folders=nil, query_parent=nil, db_parent=nil )
+  - *folders*: list of folders (optional) - array of strings
+  - *query_parent*: parent directory of folders (optional) - string
+  - *db_parent*: parent directory of database (optional) - string
+
+*notes:* '*folder*' argument can be relative to '*query_parent*'. All optional parameters must be set in the config.yml file
+
+## How to setup a Blast database for a transcriptome
+
+Using makeblastdb command that comes bundled with Blast+
+
+- Open the command line in your operating system
+- Navigate to directory
+- Go to directory that has the fasta file with the assembly
+- Run makeblastdb command in that directory
+
+  - nucleotides database
+
+    $ makeblastdb -in <filename> -dbtype nucl -out "<blast_db_new_name>" -title "<blast_db_new_name>"
+
+  - protein database
+
+    $ makeblastdb -in <filename> -dbtype nucl -out "<blast_db_new_name>" -title "<blast_db_new_name>"
+
+*note:* do to not use spaces in the <blast db new name>
+
+### Quickly setup databases in Linux and Mac OSX
+
+In Linux and OSX you can place the fasta files in db_and_queries/import_dbs directory and run the import_fastas.sh script
+
+    $ cd db_and_queries/import_dbs
+    $ sh import_fastas.sh [nucl|prot]
+
+In Windows run the import_fastas.bat script
+
+    $ cd db_and_queries/import_dbs
+    $ import_fastas.bat [nucl|prot]
+
+## Relation with other tools
+
+- [Gene Extractor](https://github.com/averissimo/gene-extractor/): can be used to extract genes from Kegg2 and GenBank using keyword search.
+- [ORF-Finder](http://github.com/averissimo/orf_finder): Finds the longest Open Reading Frame from a nucleotide sequence.
+- [MassBlast package bundler](https://github.com/averissimo/app-mass-blast): Creates a package that can be easily used in all main Operating Systems without having to install Ruby and any Ruby dependecies.
+
+## Ackowledgements
+
+This tool was created as a part of [FCT](www.fct.p) grant SFRH/BD/97415/2013 and European Commission research project [BacHBerry](www.bachberry.eu) (FP7- 613793)
+
+[Developer](http://web.tecnico.ulisboa.pt/andre.verissimo/)