updates after Olga's Testing.

docs/build/html/_sources/get-started/run/gui.rst.txt

@@ -24,7 +24,7 @@ Your prompt should show you (dicast-snakemake), to show you your conda environme
 
 .. note::
 
-  the graphical user interface assumes a X11 rendering system. If you're not on a Linux machine, find out how to host an X11 daemon for yourself. If you're using ``ssh``, please use the ``ssh -X`` flag, to allow X11 forwarding. If you're running DICAST on your local machine. the output of ``echo $DISPLAY`` should read ``:0``
+  The graphical user interface assumes a X11 rendering system. If you're using ``ssh``, please use the ``ssh -X`` flag, to allow X11 forwarding. If you're not on a Linux machine, locally, find out how to host an X11 daemon for yourself. If you're on a Mac, this could mean installing ``Xquartz`` on your localmachine.  If you're running DICAST on your local linux machine, the output of ``echo $DISPLAY`` should read ``:0``; this suggests that you have X11 forwarded correctly to your localmachine.
 
 =======================================  ==========================================================================================
 Options                                  Explanation
@@ -43,7 +43,7 @@ Close                                    Shuts down the GUI, leaving a running s
 =======================================  ==========================================================================================
 
 
-
+DICAST will continue to run, and you can safely close the GUI. Re-opening the GUI connects you back to a running instance of DICAST, if it isn't finished already.
 
 Custom Configuration file:
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -81,3 +81,9 @@ Troubleshooting
 .. warning::
 
   Aborting a run: Once the dockers begin, they're not under DICAST's control to abort. If you really want to interrupt DICAST, also check for running containers `docker ps` and stop/ kill running containers with `docker stop <container-name>`. Also use the clean up function to clean up an interrupted run.
+
+
+Interrupting a DCIAST run
+^^^^^^^^^^^^^^^^^^^^^^^^^
+
+If you want to interrupt a DICAST run. Click on the ``Abort`` button and then click on the ``Clean up`` button. DICAST unfortunately doesn't show you that this is a required step, so until ``Clean up`` is clicked upon, your next run will not start. Your configurations should stay as you set them last. Click on ``Acknowledge overwrite`` checkbox and you're all set for the next run.

docs/build/html/get-started/run.html

@@ -239,6 +239,7 @@ <h1>Run your analysis<a class="headerlink" href="#run-your-analysis" title="Perm
 <li class="toctree-l1"><a class="reference internal" href="run/gui.html">Run DICAST with a graphical user interface</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="run/gui.html#custom-configuration-file">Custom Configuration file:</a></li>
 <li class="toctree-l2"><a class="reference internal" href="run/gui.html#troubleshooting">Troubleshooting</a></li>
+<li class="toctree-l2"><a class="reference internal" href="run/gui.html#interrupting-a-dciast-run">Interrupting a DCIAST run</a></li>
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="run/dicast-cli.html">Run DICAST via Command Line Interface (depreciated)</a><ul>

docs/build/html/get-started/run/gui.html

@@ -251,7 +251,7 @@ <h1>Run DICAST with a graphical user interface<a class="headerlink" href="#run-d
 </div>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
-<p class="last">the graphical user interface assumes a X11 rendering system. If you’re not on a Linux machine, find out how to host an X11 daemon for yourself. If you’re using <code class="docutils literal notranslate"><span class="pre">ssh</span></code>, please use the <code class="docutils literal notranslate"><span class="pre">ssh</span> <span class="pre">-X</span></code> flag, to allow X11 forwarding. If you’re running DICAST on your local machine. the output of <code class="docutils literal notranslate"><span class="pre">echo</span> <span class="pre">$DISPLAY</span></code> should read <code class="docutils literal notranslate"><span class="pre">:0</span></code></p>
+<p class="last">The graphical user interface assumes a X11 rendering system. If you’re using <code class="docutils literal notranslate"><span class="pre">ssh</span></code>, please use the <code class="docutils literal notranslate"><span class="pre">ssh</span> <span class="pre">-X</span></code> flag, to allow X11 forwarding. If you’re not on a Linux machine, locally, find out how to host an X11 daemon for yourself. If you’re on a Mac, this could mean installing <code class="docutils literal notranslate"><span class="pre">Xquartz</span></code> on your localmachine.  If you’re running DICAST on your local linux machine, the output of <code class="docutils literal notranslate"><span class="pre">echo</span> <span class="pre">$DISPLAY</span></code> should read <code class="docutils literal notranslate"><span class="pre">:0</span></code>; this suggests that you have X11 forwarded correctly to your localmachine.</p>
 </div>
 <table border="1" class="docutils">
 <colgroup>
@@ -299,6 +299,7 @@ <h1>Run DICAST with a graphical user interface<a class="headerlink" href="#run-d
 </tr>
 </tbody>
 </table>
+<p>DICAST will continue to run, and you can safely close the GUI. Re-opening the GUI connects you back to a running instance of DICAST, if it isn’t finished already.</p>
 <div class="section" id="custom-configuration-file">
 <h2>Custom Configuration file:<a class="headerlink" href="#custom-configuration-file" title="Permalink to this headline">¶</a></h2>
 <p>With this, custom configure your dicast run</p>
@@ -364,6 +365,10 @@ <h2>Troubleshooting<a class="headerlink" href="#troubleshooting" title="Permalin
 <p class="last">Aborting a run: Once the dockers begin, they’re not under DICAST’s control to abort. If you really want to interrupt DICAST, also check for running containers <cite>docker ps</cite> and stop/ kill running containers with <cite>docker stop &lt;container-name&gt;</cite>. Also use the clean up function to clean up an interrupted run.</p>
 </div>
 </div>
+<div class="section" id="interrupting-a-dciast-run">
+<h2>Interrupting a DCIAST run<a class="headerlink" href="#interrupting-a-dciast-run" title="Permalink to this headline">¶</a></h2>
+<p>If you want to interrupt a DICAST run. Click on the <code class="docutils literal notranslate"><span class="pre">Abort</span></code> button and then click on the <code class="docutils literal notranslate"><span class="pre">Clean</span> <span class="pre">up</span></code> button. DICAST unfortunately doesn’t show you that this is a required step, so until <code class="docutils literal notranslate"><span class="pre">Clean</span> <span class="pre">up</span></code> is clicked upon, your next run will not start. Your configurations should stay as you set them last. Click on <code class="docutils literal notranslate"><span class="pre">Acknowledge</span> <span class="pre">overwrite</span></code> checkbox and you’re all set for the next run.</p>
+</div>
 </div>
 
 

docs/source/get-started/run/gui.rst

@@ -24,7 +24,7 @@ Your prompt should show you (dicast-snakemake), to show you your conda environme
 
 .. note::
 
-  the graphical user interface assumes a X11 rendering system. If you're not on a Linux machine, find out how to host an X11 daemon for yourself. If you're using ``ssh``, please use the ``ssh -X`` flag, to allow X11 forwarding. If you're running DICAST on your local machine. the output of ``echo $DISPLAY`` should read ``:0``
+  The graphical user interface assumes a X11 rendering system. If you're using ``ssh``, please use the ``ssh -X`` flag, to allow X11 forwarding. If you're not on a Linux machine, locally, find out how to host an X11 daemon for yourself. If you're on a Mac, this could mean installing ``Xquartz`` on your localmachine.  If you're running DICAST on your local linux machine, the output of ``echo $DISPLAY`` should read ``:0``; this suggests that you have X11 forwarded correctly to your localmachine.
 
 =======================================  ==========================================================================================
 Options                                  Explanation
@@ -43,7 +43,7 @@ Close                                    Shuts down the GUI, leaving a running s
 =======================================  ==========================================================================================
 
 
-
+DICAST will continue to run, and you can safely close the GUI. Re-opening the GUI connects you back to a running instance of DICAST, if it isn't finished already.
 
 Custom Configuration file:
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -81,3 +81,9 @@ Troubleshooting
 .. warning::
 
   Aborting a run: Once the dockers begin, they're not under DICAST's control to abort. If you really want to interrupt DICAST, also check for running containers `docker ps` and stop/ kill running containers with `docker stop <container-name>`. Also use the clean up function to clean up an interrupted run.
+
+
+Interrupting a DCIAST run
+^^^^^^^^^^^^^^^^^^^^^^^^^
+
+If you want to interrupt a DICAST run. Click on the ``Abort`` button and then click on the ``Clean up`` button. DICAST unfortunately doesn't show you that this is a required step, so until ``Clean up`` is clicked upon, your next run will not start. Your configurations should stay as you set them last. Click on ``Acknowledge overwrite`` checkbox and you're all set for the next run.

src/ASimulatoR/run_asimulator.sh

@@ -39,6 +39,7 @@ docker run --rm --name $USER-$RANDOM-dicast-$tool --user $(id -u):$(id -g) -v $a
 
 # Bringing the outputs to inputdir.
 set +e
+mkdir -P src/ASimulatoR/out/ 2>/dev/null
 mv $asimulator_outputdir/*gtf $( echo $inputdir| sed 's/\/MOUNT\///g')/ASimulatoR.gtf
 mv $asimulator_outputdir/*gff3 $( echo $inputdir| sed 's/\/MOUNT\///g')/ASimulatoR.gff3
 for i in $(ls ${asimulator_outputdir}/*fastq)