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+{#
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+/**
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+ * @file
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+ * Default theme implementation of BLAST UI Help page.
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+ */
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+#}
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+
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+<h3>Tripal BLAST Module Description</h3>
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+<p>This module provides a basic interface to allow your users to utilize your server's NCBI BLAST+.</p>
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+
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+<p>
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+ <a href="#setup">Setup</a> |
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+ <a href="#function">Functionality</a> |
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+ <a href="#protection">Large jobs |
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+ <a href="#genomeview">Genome visualization</a>
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+</p>
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+
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+<a name="setup"></a>
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+—
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+<h3><b>Setup Instructions</b></h3>
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+<ol>
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+ <li>
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+ Install NCBI BLAST+ on your server (Tested with 2.2.26+). There is a
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+ <a href="https://launchpad.net/ubuntu/+source/ncbi-blast+">package available
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+ for Ubuntu</a> to ease installation. Optionally you can set the path to your
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+ BLAST executable: {{ context_links['link_config'] }} Page.
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+ </li>
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+ <li>
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+ Optionally, create Tripal External Database References to allow you to link
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+ the records in your BLAST database to further information. To do this simply
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+ go to {{ context_links['link_dbadd'] }} and make sure to fill in the Database
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+ prefix which will be concatenated with the record IDs in your BLAST database
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+ to determine the link-out to additional information. Note that a regular
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+ expression can be used when creating the BLAST database to indicate what the
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+ ID is.
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+ </li>
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+ <li>
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+ Create "BLAST Database" {{ context_links['link_nodeadd'] }} nodes for each dataset you want to make available for your users to BLAST
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+ against. BLAST databases should first be created using the command-line
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+ <code>makeblastdb</code> program with the <code>-parse_seqids</code> flag.
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+ </li>
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+ <li>
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+ It's recommended that you also install the <a href="http://drupal.org/project/tripal_daemon">Tripal Job Daemon</a>
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+ to manage BLAST jobs and ensure they are run soon after being submitted by the
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+ user. Without this additional module, administrators will have to execute the
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+ tripal jobs either manually or through use of cron jobs.
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+ </li>
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+</ol>
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+
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+<a name="function"></a>
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+—
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+<h3><b>Highlighted Functionality</b></h3>
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+<ul>
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+ <li>Supports {{ context_links['link_blastn'] }},
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+ {{ context_links['link_blastx'] }},
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+ {{ context_links['blastp'] }} and
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+ {{ context_linkst['tblastx'] with separate forms depending upon the database/query type.
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+ </li>
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+ <li>
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+ Simple interface allowing users to paste or upload a query sequence and then
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+ select from available databases. Additionally, a FASTA file can be uploaded
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+ for use as a database to BLAST against (this functionality can be disabled).
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+ </li>
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+ <li>
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+ Tabular Results listing with alignment information and multiple download
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+ formats (HTML, TSV, XML) available.
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+ </li>
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+ <li>
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+ Completely integrated with Tripal Jobs: {{ context_links['link_jobs'] }}
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+ providing administrators with a way to track BLAST jobs and ensuring long
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+ running BLASTs will not cause page time-outs
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+ </li>
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+ <li>
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+ BLAST databases are made available to the module by creating Drupal Pages: {{ context_link['link_nodeadd'] }}
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+ describing them. This allows administrators to use the Drupal Field API to add any information they want to these pages:
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+ {{ context_links['link_dbfields'] }}
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+ </li>
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+ <li>
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+ BLAST database records can be linked to an external source with more
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+ information (ie: NCBI) per BLAST database.
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+ </li>
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+</ul>
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+
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+<a name="protection"</a></a>
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+—
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+<h3><b>Protection Against Large Jobs</b></h3>
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+Depending on the size and nature of your target databases, you may wish to constrain use
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+of this module.
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+<ol>
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+ <li>Limit the number of results displayed via admin page. The recommended number is 500.</li>
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+ <li>
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+ Limit the maximum upload file size in php settings. This is less useful because some
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+ very large queries may be manageable, and others not.
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+ </li>
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+ <li>
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+ Repeat-mask your targets, or provide repeat-masked versions. Note that some
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+ researchers may be looking for repeats, so this may limit the usefulness of the BLAST
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+ service.
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+ </li>
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+</ol>
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+
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+<a name="genomeview"></a>
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+—
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+<h3><b>Whole Genome Visualization</b></h3>
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+This module can be configured to use
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+<a href="https://github.com/LegumeFederation/cvitjs">CViTjs</a> to display BLAST hits on
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+a genome image.
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+
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+<h4>CViTjs Setup</h4>
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+<ol>
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+ <li>
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+ <a href="https://github.com/LegumeFederation/cvitjs">Download CViTjs</a> and copy
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+ the code to your webserver. It needs to be placed in <code>[your drupal root]/sites/all/libraries</code>. To download, execute
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+ the git command inside the <code>libraries/</code> directory:<br>
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+ <code>git clone https://github.com/LegumeFederation/cvitjs.git</code>
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+ </li>
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+ <li>
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+ CViTjs will have a config file in its root directory named cvit.conf. This file
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+ provides information for whole genome visualization for each genome BLAST target.
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+ <b>Make sure the config file can be edited by your web server.</b>
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+ </li>
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+ <li>
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+ Enable CViTjs from the BLAST module administration page.
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+ </li>
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+ <li>
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+ Edit the configuration file to define each genome target. These will look like:
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+ <pre>
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+[data.Cajanus cajan - genome]
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+conf = data/cajca/cajca.conf
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+defaultData = data/cajca/cajca.gff</pre>
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+ Where:<br>
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+ <ul>
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+ <li>the section name, "data.Cajanus cajan - genome", consists of "data." followed
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+ by the name of the BLAST target node,</li>
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+ <li>the file "cajca.conf" is a cvit configuration file which describes how to draw the
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+ chromosomes and BLAST hits on the <i>Cajanus cajan</i> genome,</li>
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+ <li>and the file "cajca.gff" is a GFF3 file that describes the <i>Cajanus cajan</i>
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+ chromosomes.</li>
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+ </ul>
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+ At the top of the configuration file there must be a [general] section that defines
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+ the default data set. For example:
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+ <pre>
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+[general]
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+data_default = data.Cajanus cajan - genome</pre>
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+ </li>
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+ <li>
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+ Edit the nodes for each genome target (nodes of type "BLAST Database") and enable whole
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+ genome visualization. Remember that the names listed in the CViTjs config file must
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+ match the BLAST node name. In the example above, the BLAST database node for the
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+ <i>Cajanus cajan</i> genome assembly is named "Cajanus cajan - genome"
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+ </li>
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+</ol>
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+
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+<h4>Notes</h4>
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+<ul>
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+<li>The .conf file for each genome can be modified to suit your needs and tastes. See the
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+ sample configuration file, <code>data/test1/test1.conf</code>, and the CViTjs
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+ <a href="https://github.com/LegumeFederation/cvitjs#using-cvitjs">documentation</a>.</li>
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+<li>Each blast target CViTjs configuration file must define how to visualize blast hits or you will not see them.
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+ <pre>[blast]
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+feature = BLASTRESULT:match_part
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+glyph = position
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+shape = rect
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+color = #FF00FF
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+width = 5</pre></li>
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+<li>You will have to put the target-specific conf and gff files (e.g. cajca.conf and
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+ cjca.gff) on your web server, in the directory, <code>sites/all/libraries/cvitjs/data</code>. You may
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+ choose to group files for each genome into subdirectories, for example,
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+ <code>sites/all/libraries/cvitjs/data/cajca</code>.</li>
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+<li>It is important to make sure that cvit.conf points to the correct data directory and the
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+ correct .gff and .conf files for the genome in question. For more information about how to
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+ create the .gff file, see the
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+ <a href="https://github.com/LegumeFederation/cvitjs#how-to">documentation</a>.</li>
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+</ul>
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Reynold Tan