Added help text for cvitjs conf files: [blast] stanza.

theme/blast_help.tpl.php

@@ -16,7 +16,7 @@
 <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> 
+  <a href="#setup">Setup</a> | <a href="#function">Functionality</a>
   | <a href="#protection">Large jobs | <a href="#genomeview">Genome visualization</a>
 </p>
 
@@ -25,32 +25,32 @@
 <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 
+    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 
+    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.  
+    <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 
+    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>
@@ -59,33 +59,33 @@
 &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 
+  <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 
+    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 
+    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 
+    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 
+    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 
+    BLAST database records can be linked to an external source with more
     information (ie: NCBI) per BLAST database.
   </li>
 </ul>
@@ -93,17 +93,17 @@
 <a name="protection"</a></a>
 &mdash;
 <h3><b>Protection Against Large Jobs</b></h3>
-Depending on the size and nature of your target databases, you may wish to constrain use 
+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 
+    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 
+    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>
@@ -111,19 +111,21 @@ of this module.
 <a name="genomeview"></a>
 &mdash;
 <h3><b>Whole Genome Visualization</b></h3>
-This module can be configured to use 
-<a href="https://github.com/LegumeFederation/cvitjs">CViTjs</a> to display BLAST hits on 
-a genome image. The process is as follows:
+This module can be configured to use
+<a href="https://github.com/LegumeFederation/cvitjs">CViTjs</a> to display BLAST hits on
+a genome image.
+
+<h4>CViTjs Setup</h4>
 <ol>
   <li>
     <a href="https://github.com/LegumeFederation/cvitjs">Download CViTjs</a> and copy
     the code to your webserver. It might make the most sense to put the code directly into
-    this module's directory, in a subdirectory named <code>js/</code>. To download, execute 
+    this module's directory, in a subdirectory named <code>js/</code>. To download, execute
     the git command inside the <code>js/</code> subdirectory:<br>
     <code>git clone https://github.com/LegumeFederation/cvitjs.git</code>
   </li>
   <li>
-    CViTjs will have a config file in its root directory named cvit.conf. This file 
+    CViTjs will have a config file in its root directory named cvit.conf. This file
     provides information for whole genome visualization for each genome BLAST target.
     <b>Make sure the config file can be edited by your web server.</b>
   </li>
@@ -135,7 +137,7 @@ a genome image. The process is as follows:
   </li>
   <li>
     Enable CViTjs from the BLAST module administration page and provide the path to the
-    root directory for the CViTjs code relative to this module. For example, 
+    root directory for the CViTjs code relative to this module. For example,
     <code>js/cvitjs</code>.
   </li>
   <li>
@@ -148,20 +150,11 @@ defaultData = data/cajca/cajca.gff</pre>
     <ul>
       <li>the section name, "data.Cajanus cajan - genome", consists of "data." followed
           by the name of the BLAST target node,</li>
-      <li>the file "cajca.conf" is a cvit configuration file which describes how to draw the 
+      <li>the file "cajca.conf" is a cvit configuration file which describes how to draw the
           chromosomes and BLAST hits on the <i>Cajanus cajan</i> genome,</li>
-      <li>and the file "cajca.gff" is a GFF3 file that describes the <i>Cajanus cajan</i> 
+      <li>and the file "cajca.gff" is a GFF3 file that describes the <i>Cajanus cajan</i>
           chromosomes.</li>
     </ul>
-    The .conf file for each genome can be modified to suit your needs and tastes. See the
-    sample configuration file, <code>data/test1/test1.conf</code>, and the CViTjs
-    <a href="https://github.com/LegumeFederation/cvitjs#using-cvitjs">documentation</a>
-    
-    You will have to put the target-specific conf and gff files (e.g. cajca.conf and 
-    cjca.gff) on your web server, in the directory, <code>js/cvitjs/data</code>. You may 
-    choose to group files for each genome into subdirectories, for example, 
-    <code>js/cvitjs/data/cajca</code>.
-    <br><br>
     At the top of the configuration file there must be a [general] section that defines
     the default data set. For example:
     <pre>
@@ -169,15 +162,31 @@ defaultData = data/cajca/cajca.gff</pre>
 data_default = data.Cajanus cajan - genome</pre>
   </li>
   <li>
-    Edit the nodes for each genome target (nodes of type "BLAST Database") and enable whole 
-    genome visualization. Remember that the names listed in the CViTjs config file must 
+    Edit the nodes for each genome target (nodes of type "BLAST Database") and enable whole
+    genome visualization. Remember that the names listed in the CViTjs config file must
     match the BLAST node name. In the example above, the BLAST database node for the
     <i>Cajanus cajan</i> genome assembly is named "Cajanus cajan - genome"
   </li>
 </ol>
 
-It is important to make sure that cvit.conf points to the correct data directory and the
-correct .gff and .conf files for the genome in question. For more information about how to 
-create the .gff file, see the 
-<a href="https://github.com/LegumeFederation/cvitjs#how-to">documentation</a>.
-
+<h4>Notes</h4>
+<ul>
+<li>The .conf file for each genome can be modified to suit your needs and tastes. See the
+  sample configuration file, <code>data/test1/test1.conf</code>, and the CViTjs
+  <a href="https://github.com/LegumeFederation/cvitjs#using-cvitjs">documentation</a>.</li>
+<li>Each blast target CViTjs configuration file must define how to visualize blast hits or you will not see them.
+  <pre>[blast]
+feature = BLASTRESULT:match_part
+glyph   = position
+shape = rect
+color   = #FF00FF
+width = 5</pre></li>
+<li>You will have to put the target-specific conf and gff files (e.g. cajca.conf and
+  cjca.gff) on your web server, in the directory, <code>js/cvitjs/data</code>. You may
+  choose to group files for each genome into subdirectories, for example,
+  <code>js/cvitjs/data/cajca</code>.</li>
+<li>It is important to make sure that cvit.conf points to the correct data directory and the
+  correct .gff and .conf files for the genome in question. For more information about how to
+  create the .gff file, see the
+  <a href="https://github.com/LegumeFederation/cvitjs#how-to">documentation</a>.</li>
+</ul>