Update to include releases information

README.md

@@ -3,19 +3,46 @@ MassBLAST
 
 Library to query multiple files against many databases
 
-# How to use
+# 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 (althought the binaries are 32-bits, due to our packaging tool)
+
+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 Blast+ (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.
+- run mass-blast script (either double click it on Windows or as a command in the command line.
+
+# Install and usage (from source code)
+
+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
+  $ 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
 
-        ruby bootstrap.rb
+    $ rake bootstrap.rb
 
 If you need to include it on your code use:
 
@@ -25,7 +52,7 @@ If you need to include it on your code use:
 
 ## How to test it
 
-        rake spec
+    $  rake spec
 
 ## Type of blast implemented
 
@@ -53,10 +80,31 @@ All different types have two implemented methods, blast and blast_folders
 
 *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
+
+    $ makeblastdb -in <filename> -dbtype nucl -out "<blast db new name>" -title "<blast db new name>"
+
+*note:* try 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 make_blast_db_in_for_fastas_in_directory.sh script
+
+    $ cd db_and_queries/import_dbs
+    $ sh make_blast_db_in_for_fastas_in_directory.sh
+
 ## 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