tripal_blast/theme/blast_help.tpl.php

<?php
/**
 * This template displays the help page for the BLAST UI
 */
?>

<style>
.sub_table {
  border: 0px;
  padding:1px 1px;
  background-color: inherit;
}
</style>

<h3>Tripal BLAST Module Description</h3>
<p>This module provides a basic interface to allow your users to utilize your server's NCBI BLAST+.</p>

<p>
  <a href="#setup">Setup</a> | <a href="#function">Functionality</a>
</p>

<a name="setup"></a>
&mdash;
<h3><b>Setup Instructions</b></h3>
<ol>
  <li>
    Install NCBI BLAST+ on your server (Tested with 2.2.26+). There is a 
    <a href="https://launchpad.net/ubuntu/+source/ncbi-blast+">package available 
    for Ubuntu</a> to ease installation. Optionally you can set the path to your 
    BLAST executable <a href="<?php print url('admin/tripal/extension/tripal_blast/blast_ui');?>">
    in the settings</a>.
  </li>
  <li>
    Optionally, create Tripal External Database References to allow you to link 
    the records in your BLAST database to further information. To do this simply 
    go to <a href="<?php print url('admin/tripal/chado/tripal_db/add'); ?>" target="_blank">Tripal> 
    Chado Modules > Databases > Add DB</a> and make sure to fill in the Database 
    prefix which will be concatenated with the record IDs in your BLAST database 
    to determine the link-out to additional information. Note that a regular 
    expression can be used when creating the BLAST database to indicate what the 
    ID is.
  </li>
  <li>
    <a href="<?php print url('node/add/blastdb');?>">Create "Blast Database" 
    nodes</a> for each dataset you want to make available for your users to BLAST 
    against. BLAST databases should first be created using the command-line 
    <code>makeblastdb</code> program with the <code>-parse_seqids</code> flag.  
  </li>
  <li>
    It's recommended that you also install the <a href="http://drupal.org/project/tripal_daemon">Tripal Job Daemon</a> 
    to manage BLAST jobs and ensure they are run soon after being submitted by the 
    user. Without this additional module, administrators will have to execute the 
    tripal jobs either manually or through use of cron jobs.
  </li>
</ol>

<a name="function"></a>
&mdash;
<h3><b>Highlighted Functionality</b></h3>
<ul>
  <li>Supports <a href="<?php print url('blast/nucleotide/nucleotide');?>">blastn</a>, 
    <a href="<?php print url('blast/nucleotide/protein');?>">blastx</a>, 
    <a href="<?php print url('blast/protein/protein');?>">blastp</a> and 
    <a href="<?php print url('blast/protein/nucleotide');?>">tblastx</a> with separate forms depending upon the database/query type.
  </li>
  <li>
    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 (this functionality can be disabled).
  </li>
  <li>
    Tabular Results listing with alignment information and multiple download 
    formats (HTML, TSV, XML) available.
  </li>
  <li>
    Completely integrated with <a href="<?php print url('admin/tripal/tripal_jobs');?>">Tripal Jobs</a> 
    providing administrators with a way to track BLAST jobs and ensuring long 
    running BLASTs will not cause page time-outs
  </li>
  <li>
    BLAST databases are made available to the module by 
    <a href="<?php print url('node/add/blastdb');?>">creating Drupal Pages</a> 
    describing them. This allows administrators to 
    <a href="<?php print url('admin/structure/types/manage/blastdb/fields');?>">use the Drupal Field API to add any information they want to these pages</a>.
  </li>
  <li>
    BLAST database records can be linked to an external source with more 
    information (ie: NCBI) per BLAST database.
  </li>
</ul>

<h3><b>Protection Against Large Jobs</b></h3>
Depending on the size and nature of your target databases, you may wish to constrain use 
of this module.
<ol>
  <li>Limit the number of results displayed via admin page. The recommended number is 500.</li>
  <li>
    Limit the maximum upload file size in php settings. This is less useful because some 
    very large queries may be manageable, and others not.
  </li>
  <li>
    Repeat-mask your targets, or provide repeat-masked versions. Note that some 
    researchers may be looking for repeats, so this may limit the usefulness of the BLAST 
    service.
  </li>
</ol>