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version++ to 1.3.17, render docs.
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2 changes: 1 addition & 1 deletion .version
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@@ -1 +1 @@
v1.3.17-dev
v1.3.17
2 changes: 1 addition & 1 deletion docs/GENERATED/BioLockJ-Api/index.html
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Expand Up @@ -219,7 +219,7 @@ <h1 id="biolockj-api">BioLockJ API<a class="headerlink" href="#biolockj-api" tit
<p>BioLockJ comes with an API. </p>
<p>For the most up-to-date information about how to use the API, see the help menu: </p>
<p><code>biolockj-api help</code> </p>
<pre><code>BioLockJ API v1.3.16 - UNCC Fodor Lab
<pre><code>BioLockJ API v1.3.17 - UNCC Fodor Lab

Usage:
(bash)
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6 changes: 3 additions & 3 deletions docs/GENERATED/Docker/index.html
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Expand Up @@ -231,15 +231,15 @@ <h1 id="docker">Docker<a class="headerlink" href="#docker" title="Permanent link
<tbody>
<tr>
<td align="left"><em>docker.imageName</em></td>
<td align="left"><em>string</em> <br>The name of a docker image to override whatever a module says to use.<br><em>default:</em> <em>null</em></td>
<td align="left"><em>string</em> <br>The name of a docker image to override whatever a module says to use. Only use the module-specific-override form of this property.<br><em>default:</em> <em>null</em></td>
</tr>
<tr>
<td align="left"><em>docker.imageOwner</em></td>
<td align="left"><em>string</em> <br>name of the Docker Hub user that owns the docker containers<br><em>default:</em> <em>null</em></td>
<td align="left"><em>string</em> <br>Name of the Docker Hub user that owns the docker containers. Only use the module-specific-override form of this property.<br><em>default:</em> <em>null</em></td>
</tr>
<tr>
<td align="left"><em>docker.imageTag</em></td>
<td align="left"><em>string</em> <br>indicate specific version of Docker images<br><em>default:</em> <em>null</em></td>
<td align="left"><em>string</em> <br>Image tag, a specific version of Docker images. Only use the module-specific-override form of this property.<br><em>default:</em> <em>null</em></td>
</tr>
<tr>
<td align="left"><em>docker.mountSock</em></td>
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8 changes: 4 additions & 4 deletions docs/GENERATED/General-Properties/index.html
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Expand Up @@ -348,15 +348,15 @@ <h3 id="docker"><a href="../Docker/">docker</a><a class="headerlink" href="#dock
<tbody>
<tr>
<td align="left"><em>docker.imageName</em></td>
<td align="left"><em>string</em> <br>The name of a docker image to override whatever a module says to use.<br><em>default:</em> <em>null</em></td>
<td align="left"><em>string</em> <br>The name of a docker image to override whatever a module says to use. Only use the module-specific-override form of this property.<br><em>default:</em> <em>null</em></td>
</tr>
<tr>
<td align="left"><em>docker.imageOwner</em></td>
<td align="left"><em>string</em> <br>name of the Docker Hub user that owns the docker containers<br><em>default:</em> <em>null</em></td>
<td align="left"><em>string</em> <br>Name of the Docker Hub user that owns the docker containers. Only use the module-specific-override form of this property.<br><em>default:</em> <em>null</em></td>
</tr>
<tr>
<td align="left"><em>docker.imageTag</em></td>
<td align="left"><em>string</em> <br>indicate specific version of Docker images<br><em>default:</em> <em>null</em></td>
<td align="left"><em>string</em> <br>Image tag, a specific version of Docker images. Only use the module-specific-override form of this property.<br><em>default:</em> <em>null</em></td>
</tr>
<tr>
<td align="left"><em>docker.mountSock</em></td>
Expand Down Expand Up @@ -500,7 +500,7 @@ <h3 id="metadata"><a href="../Metadata/">metadata</a><a class="headerlink" href=
</tr>
<tr>
<td align="left"><em>metadata.filePath</em></td>
<td align="left"><em>string</em> <br>If absolute file path, use file as metadata.<br>If directory path, must find exactly 1 file within, to use as metadata.<br><em>default:</em> <em>null</em></td>
<td align="left"><em>file path</em> <br>If absolute file path, use file as metadata.<br>If directory path, must find exactly 1 file within, to use as metadata.<br><em>default:</em> <em>null</em></td>
</tr>
<tr>
<td align="left"><em>metadata.nullValue</em></td>
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2 changes: 1 addition & 1 deletion docs/GENERATED/Metadata/index.html
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Expand Up @@ -249,7 +249,7 @@ <h1 id="metadata">Metadata<a class="headerlink" href="#metadata" title="Permanen
</tr>
<tr>
<td align="left"><em>metadata.filePath</em></td>
<td align="left"><em>string</em> <br>If absolute file path, use file as metadata.<br>If directory path, must find exactly 1 file within, to use as metadata.<br><em>default:</em> <em>null</em></td>
<td align="left"><em>file path</em> <br>If absolute file path, use file as metadata.<br>If directory path, must find exactly 1 file within, to use as metadata.<br><em>default:</em> <em>null</em></td>
</tr>
<tr>
<td align="left"><em>metadata.nullValue</em></td>
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5 changes: 4 additions & 1 deletion docs/GENERATED/biolockj-help/index.html
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Expand Up @@ -217,7 +217,7 @@
</code></pre>

<pre><code class="bash">
BioLockJ v1.3.16 - UNCC Fodor Lab 2021
BioLockJ v1.3.17 - UNCC Fodor Lab 2021
Usage:
(bash)
biolockj [options] &lt;config|pipeline&gt;
Expand Down Expand Up @@ -249,6 +249,9 @@
--blj_proj &lt;dir&gt; Directory that contains BioLockJ pipelines. If not supplied,
biolockj will use the value of environment variable &quot;BLJ_PROJ&quot;.

Run the test pipeline:
biolockj $BLJ/templates/myFirstPipeline/myFirstPipeline.properties


</code></pre>

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Expand Up @@ -305,7 +305,7 @@ <h2 id="citation">Citation<a class="headerlink" href="#citation" title="Permanen
PRODIGAL <br />
https://github.com/hyattpd/Prodigal/releases/download/v2.6.3/prodigal.linux </p>
<p>Module developed by Shan Sun <br />
BioLockJ v1.3.16</p>
BioLockJ v1.3.17</p>

</div>
</div>
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Expand Up @@ -323,7 +323,7 @@ <h2 id="adds-modules">Adds modules<a class="headerlink" href="#adds-modules" tit
biolockj.module.implicit.parser.r16s.RdpParser </p>
<h2 id="docker">Docker<a class="headerlink" href="#docker" title="Permanent link">#</a></h2>
<p>If running in docker, this module will run in a docker container from this image:<br></p>
<pre><code>biolockjdevteam/rdp_classifier:v1.3.16
<pre><code>biolockjdevteam/rdp_classifier:v1.3.17
</code></pre>

<p>This can be modified using the following properties:<br>
Expand All @@ -332,7 +332,7 @@ <h2 id="docker">Docker<a class="headerlink" href="#docker" title="Permanent link
<code>RdpClassifier.imageTag</code><br></p>
<h2 id="citation">Citation<a class="headerlink" href="#citation" title="Permanent link">#</a></h2>
<p>Module developed by Mike Sioda <br />
BioLockJ v1.3.16</p>
BioLockJ v1.3.17</p>

</div>
</div>
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Expand Up @@ -315,7 +315,7 @@ <h2 id="adds-modules">Adds modules<a class="headerlink" href="#adds-modules" tit
biolockj.module.implicit.parser.wgs.Humann2Parser </p>
<h2 id="docker">Docker<a class="headerlink" href="#docker" title="Permanent link">#</a></h2>
<p>If running in docker, this module will run in a docker container from this image:<br></p>
<pre><code>biolockjdevteam/humann2_classifier:v1.3.16
<pre><code>biolockjdevteam/humann2_classifier:v1.3.17
</code></pre>

<p>This can be modified using the following properties:<br>
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Expand Up @@ -303,7 +303,7 @@ <h2 id="adds-modules">Adds modules<a class="headerlink" href="#adds-modules" tit
biolockj.module.implicit.parser.wgs.Kraken2Parser </p>
<h2 id="docker">Docker<a class="headerlink" href="#docker" title="Permanent link">#</a></h2>
<p>If running in docker, this module will run in a docker container from this image:<br></p>
<pre><code>biolockjdevteam/kraken2_classifier:v1.3.16
<pre><code>biolockjdevteam/kraken2_classifier:v1.3.17
</code></pre>

<p>This can be modified using the following properties:<br>
Expand Down
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Expand Up @@ -304,7 +304,7 @@ <h2 id="adds-modules">Adds modules<a class="headerlink" href="#adds-modules" tit
biolockj.module.implicit.parser.wgs.KrakenParser </p>
<h2 id="docker">Docker<a class="headerlink" href="#docker" title="Permanent link">#</a></h2>
<p>If running in docker, this module will run in a docker container from this image:<br></p>
<pre><code>biolockjdevteam/kraken_classifier:v1.3.16
<pre><code>biolockjdevteam/kraken_classifier:v1.3.17
</code></pre>

<p>This can be modified using the following properties:<br>
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Expand Up @@ -307,7 +307,7 @@ <h2 id="adds-modules">Adds modules<a class="headerlink" href="#adds-modules" tit
biolockj.module.implicit.parser.wgs.Metaphlan2Parser </p>
<h2 id="docker">Docker<a class="headerlink" href="#docker" title="Permanent link">#</a></h2>
<p>If running in docker, this module will run in a docker container from this image:<br></p>
<pre><code>biolockjdevteam/metaphlan2_classifier:v1.3.16
<pre><code>biolockjdevteam/metaphlan2_classifier:v1.3.17
</code></pre>

<p>This can be modified using the following properties:<br>
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Expand Up @@ -282,7 +282,7 @@ <h2 id="adds-modules">Adds modules<a class="headerlink" href="#adds-modules" tit
<em>none found</em> </p>
<h2 id="docker">Docker<a class="headerlink" href="#docker" title="Permanent link">#</a></h2>
<p>If running in docker, this module will run in a docker container from this image:<br></p>
<pre><code>biolockjdevteam/biolockj_controller:v1.3.16
<pre><code>biolockjdevteam/biolockj_controller:v1.3.17
</code></pre>

<p>This can be modified using the following properties:<br>
Expand All @@ -291,7 +291,7 @@ <h2 id="docker">Docker<a class="headerlink" href="#docker" title="Permanent link
<code>ShannonDiversity.imageTag</code><br></p>
<h2 id="citation">Citation<a class="headerlink" href="#citation" title="Permanent link">#</a></h2>
<p>Module developed by Anthony Fodor <br />
BioLockJ v1.3.16</p>
BioLockJ v1.3.17</p>

</div>
</div>
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4 changes: 2 additions & 2 deletions docs/GENERATED/biolockj.module.diy/ForEachFile/index.html
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Expand Up @@ -307,15 +307,15 @@ <h2 id="adds-modules">Adds modules<a class="headerlink" href="#adds-modules" tit
<em>none found</em> </p>
<h2 id="docker">Docker<a class="headerlink" href="#docker" title="Permanent link">#</a></h2>
<p>If running in docker, this module will run in a docker container from this image:<br></p>
<pre><code>biolockjdevteam/blj_basic:v1.3.16
<pre><code>biolockjdevteam/blj_basic:v1.3.17
</code></pre>

<p>This can be modified using the following properties:<br>
<code>ForEachFile.imageOwner</code><br>
<code>ForEachFile.imageName</code><br>
<code>ForEachFile.imageTag</code><br></p>
<h2 id="citation">Citation<a class="headerlink" href="#citation" title="Permanent link">#</a></h2>
<p>BioLockJ v1.3.16 <br />
<p>BioLockJ v1.3.17 <br />
Module developed by Ivory Blakley</p>

</div>
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4 changes: 2 additions & 2 deletions docs/GENERATED/biolockj.module.diy/ForEachLevel/index.html
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Expand Up @@ -315,15 +315,15 @@ <h2 id="adds-modules">Adds modules<a class="headerlink" href="#adds-modules" tit
<em>none found</em> </p>
<h2 id="docker">Docker<a class="headerlink" href="#docker" title="Permanent link">#</a></h2>
<p>If running in docker, this module will run in a docker container from this image:<br></p>
<pre><code>biolockjdevteam/blj_basic:v1.3.16
<pre><code>biolockjdevteam/blj_basic:v1.3.17
</code></pre>

<p>This can be modified using the following properties:<br>
<code>ForEachLevel.imageOwner</code><br>
<code>ForEachLevel.imageName</code><br>
<code>ForEachLevel.imageTag</code><br></p>
<h2 id="citation">Citation<a class="headerlink" href="#citation" title="Permanent link">#</a></h2>
<p>BioLockJ v1.3.16 <br />
<p>BioLockJ v1.3.17 <br />
Module developed by Ivory Blakley</p>

</div>
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4 changes: 2 additions & 2 deletions docs/GENERATED/biolockj.module.diy/ForEachLoop/index.html
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Expand Up @@ -311,15 +311,15 @@ <h2 id="adds-modules">Adds modules<a class="headerlink" href="#adds-modules" tit
<em>none found</em> </p>
<h2 id="docker">Docker<a class="headerlink" href="#docker" title="Permanent link">#</a></h2>
<p>If running in docker, this module will run in a docker container from this image:<br></p>
<pre><code>biolockjdevteam/blj_basic:v1.3.16
<pre><code>biolockjdevteam/blj_basic:v1.3.17
</code></pre>

<p>This can be modified using the following properties:<br>
<code>ForEachLoop.imageOwner</code><br>
<code>ForEachLoop.imageName</code><br>
<code>ForEachLoop.imageTag</code><br></p>
<h2 id="citation">Citation<a class="headerlink" href="#citation" title="Permanent link">#</a></h2>
<p>BioLockJ v1.3.16 <br />
<p>BioLockJ v1.3.17 <br />
Module developed by Ivory Blakley</p>

</div>
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8 changes: 4 additions & 4 deletions docs/GENERATED/biolockj.module.diy/ForEachSample/index.html
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Expand Up @@ -239,7 +239,7 @@ <h3 id="foreachsample-properties">ForEachSample properties:<a class="headerlink"
</tr>
<tr>
<td align="left"><em>metadata.filePath</em></td>
<td align="left"><em>string</em> <br>If absolute file path, use file as metadata.<br>If directory path, must find exactly 1 file within, to use as metadata. -&gt; The row names of the metadata are used as the looping mechanism for this module.<br><em>default:</em> <em>null</em></td>
<td align="left"><em>file path</em> <br>If absolute file path, use file as metadata.<br>If directory path, must find exactly 1 file within, to use as metadata. -&gt; The row names of the metadata are used as the looping mechanism for this module.<br><em>default:</em> <em>null</em></td>
</tr>
</tbody>
</table>
Expand Down Expand Up @@ -282,7 +282,7 @@ <h3 id="general-properties-applicable-to-this-module">General properties applica
</tr>
<tr>
<td align="left"><em>metadata.filePath</em></td>
<td align="left"><em>string</em> <br>If absolute file path, use file as metadata.<br>If directory path, must find exactly 1 file within, to use as metadata. -&gt; The row names of the metadata are used as the looping mechanism for this module.<br><em>default:</em> <em>null</em></td>
<td align="left"><em>file path</em> <br>If absolute file path, use file as metadata.<br>If directory path, must find exactly 1 file within, to use as metadata. -&gt; The row names of the metadata are used as the looping mechanism for this module.<br><em>default:</em> <em>null</em></td>
</tr>
<tr>
<td align="left"><em>script.defaultHeader</em></td>
Expand Down Expand Up @@ -315,15 +315,15 @@ <h2 id="adds-modules">Adds modules<a class="headerlink" href="#adds-modules" tit
<em>none found</em> </p>
<h2 id="docker">Docker<a class="headerlink" href="#docker" title="Permanent link">#</a></h2>
<p>If running in docker, this module will run in a docker container from this image:<br></p>
<pre><code>biolockjdevteam/blj_basic:v1.3.16
<pre><code>biolockjdevteam/blj_basic:v1.3.17
</code></pre>

<p>This can be modified using the following properties:<br>
<code>ForEachSample.imageOwner</code><br>
<code>ForEachSample.imageName</code><br>
<code>ForEachSample.imageTag</code><br></p>
<h2 id="citation">Citation<a class="headerlink" href="#citation" title="Permanent link">#</a></h2>
<p>BioLockJ v1.3.16 <br />
<p>BioLockJ v1.3.17 <br />
Module developed by Ivory Blakley</p>

</div>
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4 changes: 2 additions & 2 deletions docs/GENERATED/biolockj.module.diy/GenMod/index.html
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Expand Up @@ -333,15 +333,15 @@ <h2 id="adds-modules">Adds modules<a class="headerlink" href="#adds-modules" tit
<em>none found</em> </p>
<h2 id="docker">Docker<a class="headerlink" href="#docker" title="Permanent link">#</a></h2>
<p>If running in docker, this module will run in a docker container from this image:<br></p>
<pre><code>biolockjdevteam/blj_basic:v1.3.16
<pre><code>biolockjdevteam/blj_basic:v1.3.17
</code></pre>

<p>This can be modified using the following properties:<br>
<code>GenMod.imageOwner</code><br>
<code>GenMod.imageName</code><br>
<code>GenMod.imageTag</code><br></p>
<h2 id="citation">Citation<a class="headerlink" href="#citation" title="Permanent link">#</a></h2>
<p>BioLockJ v1.3.16</p>
<p>BioLockJ v1.3.17</p>

</div>
</div>
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2 changes: 1 addition & 1 deletion docs/GENERATED/biolockj.module.diy/Rmarkdown/index.html
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Expand Up @@ -312,7 +312,7 @@ <h2 id="docker">Docker<a class="headerlink" href="#docker" title="Permanent link
<code>Rmarkdown.imageTag</code><br></p>
<h2 id="citation">Citation<a class="headerlink" href="#citation" title="Permanent link">#</a></h2>
<p>Module created by Ivory Blakley <br />
BioLockJ v1.3.16</p>
BioLockJ v1.3.17</p>

</div>
</div>
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Expand Up @@ -286,7 +286,7 @@ <h3 id="general-properties-applicable-to-this-module">General properties applica
</tr>
<tr>
<td align="left"><em>metadata.filePath</em></td>
<td align="left"><em>string</em> <br>If absolute file path, use file as metadata.<br>If directory path, must find exactly 1 file within, to use as metadata.<br><em>default:</em> <em>null</em></td>
<td align="left"><em>file path</em> <br>If absolute file path, use file as metadata.<br>If directory path, must find exactly 1 file within, to use as metadata.<br><em>default:</em> <em>null</em></td>
</tr>
<tr>
<td align="left"><em>script.defaultHeader</em></td>
Expand Down Expand Up @@ -322,7 +322,7 @@ <h2 id="adds-modules">Adds modules<a class="headerlink" href="#adds-modules" tit
<em>none found</em> </p>
<h2 id="docker">Docker<a class="headerlink" href="#docker" title="Permanent link">#</a></h2>
<p>If running in docker, this module will run in a docker container from this image:<br></p>
<pre><code>biolockjdevteam/sratoolkit:v1.3.16
<pre><code>biolockjdevteam/sratoolkit:v1.3.17
</code></pre>

<p>This can be modified using the following properties:<br>
Expand All @@ -332,7 +332,7 @@ <h2 id="docker">Docker<a class="headerlink" href="#docker" title="Permanent link
<h2 id="citation">Citation<a class="headerlink" href="#citation" title="Permanent link">#</a></h2>
<p><a href="https://github.com/ncbi/sra-tools">sra-tools</a> <br />
Module developed by Philip Badzuh <br />
BioLockJ v1.3.16</p>
BioLockJ v1.3.17</p>

</div>
</div>
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Expand Up @@ -311,7 +311,7 @@ <h2 id="adds-modules">Adds modules<a class="headerlink" href="#adds-modules" tit
<em>none found</em> </p>
<h2 id="docker">Docker<a class="headerlink" href="#docker" title="Permanent link">#</a></h2>
<p>If running in docker, this module will run in a docker container from this image:<br></p>
<pre><code>biolockjdevteam/blj_basic:v1.3.16
<pre><code>biolockjdevteam/blj_basic:v1.3.17
</code></pre>

<p>This can be modified using the following properties:<br>
Expand All @@ -320,7 +320,7 @@ <h2 id="docker">Docker<a class="headerlink" href="#docker" title="Permanent link
<code>SraMetaDB.imageTag</code><br></p>
<h2 id="citation">Citation<a class="headerlink" href="#citation" title="Permanent link">#</a></h2>
<p>Module developed by Malcolm Zapatas and Ivory Blakley <br />
BioLockJ v1.3.16</p>
BioLockJ v1.3.17</p>

</div>
</div>
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Expand Up @@ -303,7 +303,7 @@ <h2 id="adds-modules">Adds modules<a class="headerlink" href="#adds-modules" tit
<em>none found</em> </p>
<h2 id="docker">Docker<a class="headerlink" href="#docker" title="Permanent link">#</a></h2>
<p>If running in docker, this module will run in a docker container from this image:<br></p>
<pre><code>biolockjdevteam/pysradb:v1.3.16
<pre><code>biolockjdevteam/pysradb:v1.3.17
</code></pre>

<p>This can be modified using the following properties:<br>
Expand All @@ -312,7 +312,7 @@ <h2 id="docker">Docker<a class="headerlink" href="#docker" title="Permanent link
<code>SraMetaData.imageTag</code><br></p>
<h2 id="citation">Citation<a class="headerlink" href="#citation" title="Permanent link">#</a></h2>
<p>Module developed by Malcolm Zapatas and Ivory Blakley <br />
BioLockJ v1.3.16</p>
BioLockJ v1.3.17</p>

</div>
</div>
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Expand Up @@ -317,7 +317,7 @@ <h2 id="docker">Docker<a class="headerlink" href="#docker" title="Permanent link
<code>SrpSrrConverter.imageTag</code><br></p>
<h2 id="citation">Citation<a class="headerlink" href="#citation" title="Permanent link">#</a></h2>
<p>Module developed by Malcolm Zapatas and Ivory Blakley <br />
BioLockJ v1.3.16</p>
BioLockJ v1.3.17</p>

</div>
</div>
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