Switched to github markdown for README

README.txt → README.md

@@ -1,66 +1,64 @@
 
-
-################################################################################
 INTRODUCTION
 ------------
-This module provides a basic interface to allow your users to utilize your 
+This module provides a basic interface to allow your users to utilize your
 server's NCBI BLAST+.
 
-Specifically it provides two forms, one for nucleotide queries and another for 
-protein queries. Currently only blastn and blastp are supported but in the future 
-you will be able to select either a nucleotide or a protein database to BLAST 
-against regardless of the type of query and this module will decide which BLAST 
-program to use based on the combination of query/database type (ie: if you 
-selected a protein database on the nucleotide BLAST form then blastx would 
+Specifically it provides two forms, one for nucleotide queries and another for
+protein queries. Currently only blastn and blastp are supported but in the future
+you will be able to select either a nucleotide or a protein database to BLAST
+against regardless of the type of query and this module will decide which BLAST
+program to use based on the combination of query/database type (ie: if you
+selected a protein database on the nucleotide BLAST form then blastx would
 be used).
 
-BLAST submissions result in the creation of Tripal jobs which then need to run 
-from the command-line. This ensures that long running BLASTS will not cause 
-page time-outs but does add some management overhead and might result in longer 
-waits for users depending on how often you have cron set to run Tripal jobs. 
-A Tripal Jobs Daemon is under development to allow these jobs to be run almost 
+BLAST submissions result in the creation of Tripal jobs which then need to run
+from the command-line. This ensures that long running BLASTS will not cause
+page time-outs but does add some management overhead and might result in longer
+waits for users depending on how often you have cron set to run Tripal jobs.
+A Tripal Jobs Daemon is under development to allow these jobs to be run almost
 as soon as they are submitted.
 
-The BLAST results page is an expandable summary table with each hit being 
-listed as a row in the table with query/hit/e-value information. The row can 
-then be expanded to include additional information including the alignment. 
-Download formats are under development to allow users to download these 
+The BLAST results page is an expandable summary table with each hit being
+listed as a row in the table with query/hit/e-value information. The row can
+then be expanded to include additional information including the alignment.
+Download formats are under development to allow users to download these
 results in the familiar tabular or HTML NCBI formats.
 
 Highlighted Functionality
 -------------------------
- - Supports blastn and blastp with separate forms depending upon the query 
+ - Supports blastn and blastp with separate forms depending upon the query
    type.
- - Simple interface allowing users to paste or upload a query sequence and 
-   then select from available databases. Additionally, a FASTA file can be 
+ - Simple interface allowing users to paste or upload a query sequence and
+   then select from available databases. Additionally, a FASTA file can be
    uploaded for use as a database to BLAST against.
  - Tabular Results listing with alignment information available.
- - Completely integrated with Tripal Jobs providing administrators with a 
-   way to track BLAST jobs and ensuring long running BLASTs will not cause 
+ - Completely integrated with Tripal Jobs providing administrators with a
+   way to track BLAST jobs and ensuring long running BLASTs will not cause
    page time-outs
- - BLAST databases are made available to the module by creating Drupal Pages 
-   describing them. This allows administrators to use the Drupal Field API to 
+ - BLAST databases are made available to the module by creating Drupal Pages
+   describing them. This allows administrators to use the Drupal Field API to
    add any information they want to these pages.
 
 Installation
 ------------
-1. Install NCBI BLAST+ on your server (Tested with 2.2.26+). There is a 
+1. Install NCBI BLAST+ on your server (Tested with 2.2.26+). There is a
    package available for Ubuntu to ease installation.
-2. Install this module as you would any Drupal module (ie: download, unpack 
+2. Install this module as you would any Drupal module (ie: download, unpack
    in sites/all/modules and enable through http://[your site]/admin/modules)
-3. Create "Blast Database" nodes for each dataset you want to make available 
-   for your users to BLAST against. BLAST databases should first be created 
+3. Create "Blast Database" nodes for each dataset you want to make available
+   for your users to BLAST against. BLAST databases should first be created
    using the command-line makeblastdb program with the -parse_seqids flag.
 
 Customization
 -------------
-The BLAST module forms can be styled using CSS stylesheets in your own theme. 
-By default it will use the default form themeing provided by your particular 
-Drupal site allowing it to feel consistent with the look-and-feel of your 
+The BLAST module forms can be styled using CSS stylesheets in your own theme.
+By default it will use the default form themeing provided by your particular
+Drupal site allowing it to feel consistent with the look-and-feel of your
 Tripal site without customization being needed.
 
-Additionally, the results page, waiting pages and the alignment section of 
-the results page have their own template files (blast_report.tpl.php, 
-blast_report_pending.tpl.php, and blast_report_alignment_row.tpl.php, 
-respectively) which can easily be overridden in your own theme providing 
+Additionally, the results page, waiting pages and the alignment section of
+the results page have their own template files (blast_report.tpl.php,
+blast_report_pending.tpl.php, and blast_report_alignment_row.tpl.php,
+respectively) which can easily be overridden in your own theme providing
 complete control over the look of the BLAST results.