Documentation update.

docs/build/html/_sources/contents.rst.txt

@@ -45,8 +45,8 @@ DICAST is currently hosted on `bioRxiv`_, at this link <notsubmitted-yet>.
 	:caption: Get started
 
 	get-started/setup
-	get-started/run
 	get-started/config
+	get-started/run
 
 
 .. toctree::

docs/build/html/_sources/get-started/config.rst.txt

@@ -1,13 +1,19 @@
 Configuring DICAST
 ====================
 
+Before running DICAST, please take some time to configure it for your first run.  
+
 DICAST is best :doc:`run with the GUI <run/gui>`, which automates the configuration of :guilabel:`scripts/snakemake/snakemake_config.yaml`, :guilabel:`scripts/config.sh` & :guilabel:`scripts/asevent_config.sh`,
-for a quick run of DICAST without simulated data, on your experiments. If you'd like to run DICAST :doc:`via CLI <run/dicast-cli>`, then edit these configuration files manually.
+for a quick run of DICAST without simulated data, on your experiments. 
+
+DICAST can be run :doc:`via CLI <run/dicast-cli>`, however, this feature is currently in development.
 
 If you'd like to modify the **Simulated dataset**, please modify :guilabel:`scripts/ASimulatoR_config.R` (See :doc:`ASimulatoR Parameters <config/ASimulatoR_parameters>`)
 
 If you'd like to run DICAST with just one tool :doc:`via docker <run/one_tool>`, then the files you need to modify are: :guilabel:`scripts/config.sh`, :guilabel:`scripts/asevent_config.sh`
 
+It's recommended to take a closer look at the config files on disk before your first run.
+
 The following files are all the configuration files found in DICAST:
   | :guilabel:`scripts/snakemake/snakemake_config.yaml`,
   | :guilabel:`scripts/ASimulatoR_config.R`,

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

@@ -3,7 +3,7 @@ Run your analysis
 
 .. note::
 
-  This guide assumes that you have followed all four pages of the :doc:`setup<setup>` carefully.
+  This guide page assumes that you have followed all four pages of the :doc:`setup<setup>` carefully and that you have :doc:`configred DICAST<setup>`.
 
 .. toctree::
    :maxdepth: 2

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

@@ -1,5 +1,5 @@
-Run DICAST via Command Line Interface (CLI)
-============================================
+Run DICAST via Command Line Interface (depreciated)
+===================================================
 
 In this section we will explain how to use DICAST to run a whole pipeline on the terminal alone.
 
@@ -43,6 +43,10 @@ Argument                               Explanation
 
 For more information, see the `Snakemake documentation <https://snakemake.readthedocs.io/en/stable/>`_.
 
+.. warning::
+
+  This feature has been depreciated and needs another Snakefile, without the ``Possible_overwrite_acknowledge`` rule. We keep this documentation here, for future support and to show you how the tool works under the hood.
+
 Troubleshooting
 ^^^^^^^^^^^^^^^
 

docs/build/html/_sources/get-started/setup/input.rst.txt

@@ -86,8 +86,12 @@ The sample_input is a template of what the files should look like. Let's however
 
   All files, including references and fastq files must be unzipped, as most of the tools within dicast require them in unzipped form.
 
+.. note::
+
+  If you work with the human genome or would like to just test if DICAST is installed well, check out the script at ``initializing-dicast.sh``  and execute it with the command ``bash initializing-dicast.sh``, to populate your input directory with relavent human references.
+
 .. note::
 
   casedir, is currently unsupported. DICAST was built originally with a design that included tools for  differential analysis. It maintains the directory structure in order to expand, to cover differential tools in the future.
 
-``example_*.sam``: DICAST can map your fastq files for you with a mapper of your choice, the results of such mapping will be found here in this directory ``bamdir``. If you have already mapped bam/sam files, place them in the bamdir, for DICAST to start from here.
+``example_*.sam``: DICAST can map your fastq files for you with a mapper of your choice, the results of such mapping will be found here in this directory ``bamdir``. If you have already mapped bam/sam files, place them in the ``input/controldir/bamdir``, for DICAST to start from here.

docs/build/html/contents.html

@@ -103,11 +103,18 @@
 </li>
 </ul>
 </li>
+<li class="toctree-l1"><a class="reference internal" href="get-started/config.html">Configuring DICAST</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="get-started/config/snakemake_parameters.html">Snakemake parameters</a></li>
+<li class="toctree-l2"><a class="reference internal" href="get-started/config/ASimulatoR_parameters.html">ASimulatoR parameters</a></li>
+<li class="toctree-l2"><a class="reference internal" href="get-started/config/general_parameters.html">Tool core parameters</a></li>
+<li class="toctree-l2"><a class="reference internal" href="get-started/config/as_parameters.html">Alternative splicing tools parameters</a></li>
+</ul>
+</li>
 <li class="toctree-l1"><a class="reference internal" href="get-started/run.html">Run your analysis</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="get-started/run/gui.html">Run DICAST with a graphical user interface</a><ul class="simple">
 </ul>
 </li>
-<li class="toctree-l2"><a class="reference internal" href="get-started/run/dicast-cli.html">Run DICAST via Command Line Interface (CLI)</a><ul class="simple">
+<li class="toctree-l2"><a class="reference internal" href="get-started/run/dicast-cli.html">Run DICAST via Command Line Interface (depreciated)</a><ul class="simple">
 </ul>
 </li>
 <li class="toctree-l2"><a class="reference internal" href="get-started/run/one_tool.html">Run one specific tool via Docker</a><ul class="simple">
@@ -116,13 +123,6 @@
 <li class="toctree-l2"><a class="reference internal" href="get-started/run/outputs.html">DICAST Outputs</a></li>
 </ul>
 </li>
-<li class="toctree-l1"><a class="reference internal" href="get-started/config.html">Configuring DICAST</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="get-started/config/snakemake_parameters.html">Snakemake parameters</a></li>
-<li class="toctree-l2"><a class="reference internal" href="get-started/config/ASimulatoR_parameters.html">ASimulatoR parameters</a></li>
-<li class="toctree-l2"><a class="reference internal" href="get-started/config/general_parameters.html">Tool core parameters</a></li>
-<li class="toctree-l2"><a class="reference internal" href="get-started/config/as_parameters.html">Alternative splicing tools parameters</a></li>
-</ul>
-</li>
 </ul>
 <p class="caption"><span class="caption-text">Tools</span></p>
 <ul>

docs/build/html/further-information/about.html

@@ -103,11 +103,18 @@
 </li>
 </ul>
 </li>
+<li class="toctree-l1"><a class="reference internal" href="../get-started/config.html">Configuring DICAST</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="../get-started/config/snakemake_parameters.html">Snakemake parameters</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../get-started/config/ASimulatoR_parameters.html">ASimulatoR parameters</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../get-started/config/general_parameters.html">Tool core parameters</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../get-started/config/as_parameters.html">Alternative splicing tools parameters</a></li>
+</ul>
+</li>
 <li class="toctree-l1"><a class="reference internal" href="../get-started/run.html">Run your analysis</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="../get-started/run/gui.html">Run DICAST with a graphical user interface</a><ul class="simple">
 </ul>
 </li>
-<li class="toctree-l2"><a class="reference internal" href="../get-started/run/dicast-cli.html">Run DICAST via Command Line Interface (CLI)</a><ul class="simple">
+<li class="toctree-l2"><a class="reference internal" href="../get-started/run/dicast-cli.html">Run DICAST via Command Line Interface (depreciated)</a><ul class="simple">
 </ul>
 </li>
 <li class="toctree-l2"><a class="reference internal" href="../get-started/run/one_tool.html">Run one specific tool via Docker</a><ul class="simple">
@@ -116,13 +123,6 @@
 <li class="toctree-l2"><a class="reference internal" href="../get-started/run/outputs.html">DICAST Outputs</a></li>
 </ul>
 </li>
-<li class="toctree-l1"><a class="reference internal" href="../get-started/config.html">Configuring DICAST</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="../get-started/config/snakemake_parameters.html">Snakemake parameters</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../get-started/config/ASimulatoR_parameters.html">ASimulatoR parameters</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../get-started/config/general_parameters.html">Tool core parameters</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../get-started/config/as_parameters.html">Alternative splicing tools parameters</a></li>
-</ul>
-</li>
 </ul>
 <p class="caption"><span class="caption-text">Tools</span></p>
 <ul>

docs/build/html/further-information/example-files.html

@@ -104,11 +104,18 @@
 </li>
 </ul>
 </li>
+<li class="toctree-l1"><a class="reference internal" href="../get-started/config.html">Configuring DICAST</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="../get-started/config/snakemake_parameters.html">Snakemake parameters</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../get-started/config/ASimulatoR_parameters.html">ASimulatoR parameters</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../get-started/config/general_parameters.html">Tool core parameters</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../get-started/config/as_parameters.html">Alternative splicing tools parameters</a></li>
+</ul>
+</li>
 <li class="toctree-l1"><a class="reference internal" href="../get-started/run.html">Run your analysis</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="../get-started/run/gui.html">Run DICAST with a graphical user interface</a><ul class="simple">
 </ul>
 </li>
-<li class="toctree-l2"><a class="reference internal" href="../get-started/run/dicast-cli.html">Run DICAST via Command Line Interface (CLI)</a><ul class="simple">
+<li class="toctree-l2"><a class="reference internal" href="../get-started/run/dicast-cli.html">Run DICAST via Command Line Interface (depreciated)</a><ul class="simple">
 </ul>
 </li>
 <li class="toctree-l2"><a class="reference internal" href="../get-started/run/one_tool.html">Run one specific tool via Docker</a><ul class="simple">
@@ -117,13 +124,6 @@
 <li class="toctree-l2"><a class="reference internal" href="../get-started/run/outputs.html">DICAST Outputs</a></li>
 </ul>
 </li>
-<li class="toctree-l1"><a class="reference internal" href="../get-started/config.html">Configuring DICAST</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="../get-started/config/snakemake_parameters.html">Snakemake parameters</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../get-started/config/ASimulatoR_parameters.html">ASimulatoR parameters</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../get-started/config/general_parameters.html">Tool core parameters</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../get-started/config/as_parameters.html">Alternative splicing tools parameters</a></li>
-</ul>
-</li>
 </ul>
 <p class="caption"><span class="caption-text">Tools</span></p>
 <ul>

docs/build/html/further-information/faq.html

@@ -104,11 +104,18 @@
 </li>
 </ul>
 </li>
+<li class="toctree-l1"><a class="reference internal" href="../get-started/config.html">Configuring DICAST</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="../get-started/config/snakemake_parameters.html">Snakemake parameters</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../get-started/config/ASimulatoR_parameters.html">ASimulatoR parameters</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../get-started/config/general_parameters.html">Tool core parameters</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../get-started/config/as_parameters.html">Alternative splicing tools parameters</a></li>
+</ul>
+</li>
 <li class="toctree-l1"><a class="reference internal" href="../get-started/run.html">Run your analysis</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="../get-started/run/gui.html">Run DICAST with a graphical user interface</a><ul class="simple">
 </ul>
 </li>
-<li class="toctree-l2"><a class="reference internal" href="../get-started/run/dicast-cli.html">Run DICAST via Command Line Interface (CLI)</a><ul class="simple">
+<li class="toctree-l2"><a class="reference internal" href="../get-started/run/dicast-cli.html">Run DICAST via Command Line Interface (depreciated)</a><ul class="simple">
 </ul>
 </li>
 <li class="toctree-l2"><a class="reference internal" href="../get-started/run/one_tool.html">Run one specific tool via Docker</a><ul class="simple">
@@ -117,13 +124,6 @@
 <li class="toctree-l2"><a class="reference internal" href="../get-started/run/outputs.html">DICAST Outputs</a></li>
 </ul>
 </li>
-<li class="toctree-l1"><a class="reference internal" href="../get-started/config.html">Configuring DICAST</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="../get-started/config/snakemake_parameters.html">Snakemake parameters</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../get-started/config/ASimulatoR_parameters.html">ASimulatoR parameters</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../get-started/config/general_parameters.html">Tool core parameters</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../get-started/config/as_parameters.html">Alternative splicing tools parameters</a></li>
-</ul>
-</li>
 </ul>
 <p class="caption"><span class="caption-text">Tools</span></p>
 <ul>

docs/build/html/genindex.html

@@ -103,11 +103,18 @@
 </li>
 </ul>
 </li>
+<li class="toctree-l1"><a class="reference internal" href="get-started/config.html">Configuring DICAST</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="get-started/config/snakemake_parameters.html">Snakemake parameters</a></li>
+<li class="toctree-l2"><a class="reference internal" href="get-started/config/ASimulatoR_parameters.html">ASimulatoR parameters</a></li>
+<li class="toctree-l2"><a class="reference internal" href="get-started/config/general_parameters.html">Tool core parameters</a></li>
+<li class="toctree-l2"><a class="reference internal" href="get-started/config/as_parameters.html">Alternative splicing tools parameters</a></li>
+</ul>
+</li>
 <li class="toctree-l1"><a class="reference internal" href="get-started/run.html">Run your analysis</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="get-started/run/gui.html">Run DICAST with a graphical user interface</a><ul class="simple">
 </ul>
 </li>
-<li class="toctree-l2"><a class="reference internal" href="get-started/run/dicast-cli.html">Run DICAST via Command Line Interface (CLI)</a><ul class="simple">
+<li class="toctree-l2"><a class="reference internal" href="get-started/run/dicast-cli.html">Run DICAST via Command Line Interface (depreciated)</a><ul class="simple">
 </ul>
 </li>
 <li class="toctree-l2"><a class="reference internal" href="get-started/run/one_tool.html">Run one specific tool via Docker</a><ul class="simple">
@@ -116,13 +123,6 @@
 <li class="toctree-l2"><a class="reference internal" href="get-started/run/outputs.html">DICAST Outputs</a></li>
 </ul>
 </li>
-<li class="toctree-l1"><a class="reference internal" href="get-started/config.html">Configuring DICAST</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="get-started/config/snakemake_parameters.html">Snakemake parameters</a></li>
-<li class="toctree-l2"><a class="reference internal" href="get-started/config/ASimulatoR_parameters.html">ASimulatoR parameters</a></li>
-<li class="toctree-l2"><a class="reference internal" href="get-started/config/general_parameters.html">Tool core parameters</a></li>
-<li class="toctree-l2"><a class="reference internal" href="get-started/config/as_parameters.html">Alternative splicing tools parameters</a></li>
-</ul>
-</li>
 </ul>
 <p class="caption"><span class="caption-text">Tools</span></p>
 <ul>