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diff --git a/docs/build/doctrees/contents.doctree b/docs/build/doctrees/contents.doctree
diff --git a/docs/build/doctrees/environment.pickle b/docs/build/doctrees/environment.pickle
diff --git a/docs/build/doctrees/further-information/example-files.doctree b/docs/build/doctrees/further-information/example-files.doctree
diff --git a/docs/build/doctrees/get-started/config.doctree b/docs/build/doctrees/get-started/config.doctree
diff --git a/docs/build/doctrees/get-started/config/general_parameters.doctree b/docs/build/doctrees/get-started/config/general_parameters.doctree
diff --git a/docs/build/doctrees/get-started/run.doctree b/docs/build/doctrees/get-started/run.doctree
diff --git a/docs/build/doctrees/get-started/run/dicast-cli.doctree b/docs/build/doctrees/get-started/run/dicast-cli.doctree
diff --git a/docs/build/doctrees/get-started/run/gui.doctree b/docs/build/doctrees/get-started/run/gui.doctree
diff --git a/docs/build/doctrees/get-started/run/one_tool.doctree b/docs/build/doctrees/get-started/run/one_tool.doctree
diff --git a/docs/build/doctrees/get-started/run/outputs.doctree b/docs/build/doctrees/get-started/run/outputs.doctree
diff --git a/docs/build/doctrees/get-started/setup/docker.doctree b/docs/build/doctrees/get-started/setup/docker.doctree
diff --git a/docs/build/html/_images/upset_plot.png b/docs/build/html/_images/upset_plot.png
diff --git a/docs/build/html/_sources/contents.rst.txt b/docs/build/html/_sources/contents.rst.txt
@@ -11,7 +11,7 @@ To provide a fair baseline while maintaining easy usability, per default we run
 The tools included here are the most widely used and well maintained among AS event detection tools. If you would like to include your tool in the pipeline please let us know.
 We hope this collection can be a starting point for future benchmarking approaches and quality control.
 
-.. figure:: /img/Screenshot_dicast.png
+.. figure:: /img/pipeline.png
 
 
 What is DICAST?

diff --git a/docs/build/html/_sources/further-information/example-files.rst.txt b/docs/build/html/_sources/further-information/example-files.rst.txt
@@ -35,15 +35,15 @@ Running multiple mapping tools (E.g., STAR, HISAT2 and bbmap)
 .. prompt:: bash
 
    cd /path/to/DICAST/input
-   wget http://ftp.ensembl.org/pub/release-104/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz
+   wget http://ftp.ensembl.org/pub/release-105/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz
    gunzip Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz
 
 6. Download or copy the genome gtf annotation into the `input` folder. Dont't forget to uncompress it. E.g.:
 
 .. prompt:: bash
 
-   wget http://ftp.ensembl.org/pub/release-104/gtf/homo_sapiens/Homo_sapiens.GRCh38.104.gtf.gz
-   gunzip Homo_sapiens.GRCh38.104.gtf.gz
+   wget http://ftp.ensembl.org/pub/release-105/gtf/homo_sapiens/Homo_sapiens.GRCh38.105.gtf.gz
+   gunzip Homo_sapiens.GRCh38.105.gtf.gz
 
 7. Download or copy the fastq files you want to align into the `/path/to/DICAST/input/controldir/fastqdir`. Note: we support only paired-end RNA-Seq - fastq files have to be in pairs.
 
@@ -60,7 +60,7 @@ In the `config.sh` file edit the following lines:
 
    read_length=76
    fastaname=Homo_sapiens.GRCh38.dna.primary_assembly.fa
-   gtfname=Homo_sapiens.GRCh38.104.gtf
+   gtfname=Homo_sapiens.GRCh38.105.gtf
 
 9. List the mapping tools you want to run:
 
@@ -119,22 +119,22 @@ Running multiple alternative splicing event detection tools (E.g., MAJIQ and Whi
 .. prompt:: bash
 
    cd /path/to/DICAST/input
-   wget http://ftp.ensembl.org/pub/release-104/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz
+   wget http://ftp.ensembl.org/pub/release-105/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz
    gunzip Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz
 
 6. Download or copy the genome annotation file into the `input` folder. Dont't forget to uncompress it. E.g.:
 
 .. prompt:: bash
 
-   wget http://ftp.ensembl.org/pub/release-104/gtf/homo_sapiens/Homo_sapiens.GRCh38.104.gtf.gz
-   gunzip Homo_sapiens.GRCh38.104.gtf.gz
+   wget http://ftp.ensembl.org/pub/release-105/gtf/homo_sapiens/Homo_sapiens.GRCh38.105.gtf.gz
+   gunzip Homo_sapiens.GRCh38.105.gtf.gz
 
 7. Download or copy the genome gff3 annotation into the `input` folder (for MAJIQ). Dont't forget to uncompress it. E.g.:
 
 .. prompt:: bash
 
-   wget http://ftp.ensembl.org/pub/release-104/gff3/homo_sapiens/Homo_sapiens.GRCh38.104.gff3.gz
-   gunzip Homo_sapiens.GRCh38.104.gff3.gz
+   wget http://ftp.ensembl.org/pub/release-105/gff3/homo_sapiens/Homo_sapiens.GRCh38.105.gff3.gz
+   gunzip Homo_sapiens.GRCh38.105.gff3.gz
 
 8. Download or copy the fastq files you want to use into the `/path/to/DICAST/input/controldir/fastqdir`. Note: we support only paired-end RNA-Seq - fastq files have to be in pairs.
 
@@ -153,8 +153,8 @@ In the `config.sh` file edit the following lines:
 
    read_length=76
    fastaname=Homo_sapiens.GRCh38.dna.primary_assembly.fa
-   gtfname=Homo_sapiens.GRCh38.104.gtf
-   gffname=Homo_sapiens.GRCh38.104.gff3
+   gtfname=Homo_sapiens.GRCh38.105.gtf
+   gffname=Homo_sapiens.GRCh38.105.gff3
 
 11. List the mapping tools you want to run:
 

diff --git a/docs/build/html/_sources/get-started/config.rst.txt b/docs/build/html/_sources/get-started/config.rst.txt
@@ -85,12 +85,12 @@ ncores
 Input Parameters
 ^^^^^^^^^^^^^^^^
 asimulator_gtf
-	| the genome gtf annotation that you use to simulate the data. Default: 'Homo_sapiens.GRCh38.104.gtf'.
+	| the genome gtf annotation that you use to simulate the data. Default: 'Homo_sapiens.GRCh38.105.gtf'.
 fastaname
 	| the genome reference file. Default: 'Homo_sapiens.GRCh38.dna.primary_assembly.fa'.
 gtfname
 	| the genome gtf annotation that you use for mapping and alternative splicing analysis. If you’re using ASimulatoR, leave this as ASimulatoR.gtf.
 gffname
 	| the genome gff3 annotation that you use for mapping and alternative splicing analysis. If you’re using ASimulatoR, leave this as ASimulatoR.gff3.
 
-The reference genome, annotation file and gff3 files could be downloaded from `Ensembl <http://ftp.ensembl.org/pub/release-104/>`_.
+The reference genome, annotation file and gff3 files could be downloaded from `Ensembl <http://ftp.ensembl.org/pub/release-105/>`_.
diff --git a/docs/build/html/_sources/get-started/config/general_parameters.rst.txt b/docs/build/html/_sources/get-started/config/general_parameters.rst.txt
@@ -106,7 +106,7 @@ ASimulatoR Parameters
 
 asimulator_gtf
   | Name of the file in the input directory used by ASimulatoR to generate new transcripts
-  | Example: ``Homo_sapiens.GRCh38.104.gtf``
+  | Example: ``Homo_sapiens.GRCh38.105.gtf``
 
 
 Input Parameters

diff --git a/docs/build/html/_sources/get-started/run.rst.txt b/docs/build/html/_sources/get-started/run.rst.txt
@@ -8,9 +8,9 @@ Run your analysis
 .. toctree::
    :maxdepth: 2
 
-   run/gui
    run/dicast-cli
    run/one_tool
+   run/gui
    run/outputs
 
 

diff --git a/docs/build/html/_sources/get-started/run/dicast-cli.rst.txt b/docs/build/html/_sources/get-started/run/dicast-cli.rst.txt
@@ -1,5 +1,5 @@
-Run DICAST via Command Line Interface (depreciated)
-===================================================
+Run DICAST via Command Line Interface 
+======================================
 
 In this section we will explain how to use DICAST to run a whole pipeline on the terminal alone.
 

diff --git a/docs/build/html/_sources/get-started/run/gui.rst.txt b/docs/build/html/_sources/get-started/run/gui.rst.txt
@@ -1,5 +1,5 @@
-Run DICAST with a graphical user interface
-================================================
+Run DICAST with a graphical user interface (depreciated)
+========================================================
 
 .. toctree::
    :maxdepth: 1

diff --git a/docs/build/html/_sources/get-started/run/one_tool.rst.txt b/docs/build/html/_sources/get-started/run/one_tool.rst.txt
@@ -16,7 +16,7 @@ If you have already built the image with <tool>:<tag> (see the :doc:`docker setu
   # If you are using our directory structure for your input and are in the dockers directory:
   # Add the --rm flag to remove container, after run.
 
-  docker run -v ./:/MOUNT --user $(id -u):$(id -g) --rm gsnap:0.1
+  docker run -v $(pwd):/MOUNT --user $(id -u):$(id -g) --rm gsnap:0.1
 
 
 Troubleshooting

diff --git a/docs/build/html/_sources/get-started/run/outputs.rst.txt b/docs/build/html/_sources/get-started/run/outputs.rst.txt
@@ -38,7 +38,7 @@ DICAST also provides a :guilabel:`output/<astoolname>-output/<Fastq-filename>_ou
 
 ------------------------------
 
-DICAST also outputs an upset plot for each ``Fastq-filename``-``mapping_tool`` combination.
+DICAST also outputs an UpSet plot for each ``Fastq-filename``-``mapping_tool`` combination.
 
 .. figure:: ../../img/upset_plot.png
 

diff --git a/docs/build/html/_sources/get-started/setup/docker.rst.txt b/docs/build/html/_sources/get-started/setup/docker.rst.txt
@@ -64,9 +64,18 @@ We support Docker version 19 and above.
 
   docker-compose --version
 
+2. Pull docker images (Not needed with snakemake)
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Should the tool you intended to run, not build locally, it's also possible to pull them from DICAST's dockerhub repository at: https://hub.docker.com/repository/docker/dicastproj/dicast
 
 
-2. Build docker images (Optional)
+.. prompt:: bash $
+
+  docker pull dicastproj/dicast:tagname
+
+
+3. Build docker images (For Developers)
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 While the steps described in this section are handled by DICAST's graphical interface, it can also be accessed via command line, for more control.
 
@@ -101,17 +110,6 @@ Where <tool> needs to be replaced with one or more of the following tools:
 
 bbmap, contextmap, crac, dart, gsnap, hisat, mapsplice, minimap, segemehl, star, subjunc, asgal, aspli, eventpointer, irfinder, majiq, sgseq, spladder, whippet
 
-
-3. Pull docker images (Fail safe)
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-Should the tool you intended to run, not build locally, it's also possible to pull them from DICAST's dockerhub repository at: https://hub.docker.com/repository/docker/dicastproj/dicast
-
-
-.. prompt:: bash $
-
-  docker pull dicastproj/dicast:tagname
-
 4. Other helpful commands
 ^^^^^^^^^^^^^^^^^^^^^^^^^
 To gracefully stop a running docker container (If perhaps snakemake's process had to be killed):

diff --git a/docs/build/html/contents.html b/docs/build/html/contents.html
@@ -67,13 +67,13 @@
 </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">
+<li class="toctree-l2"><a class="reference internal" href="get-started/run/dicast-cli.html">Run DICAST via Command Line 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 (depreciated)</a><ul class="simple">
+<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">
 </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">
+<li class="toctree-l2"><a class="reference internal" href="get-started/run/gui.html">Run DICAST with a graphical user interface (depreciated)</a><ul class="simple">
 </ul>
 </li>
 <li class="toctree-l2"><a class="reference internal" href="get-started/run/outputs.html">DICAST Outputs</a></li>
@@ -153,7 +153,7 @@ <h1>Welcome to DICAST!<a class="headerlink" href="#welcome-to-dicast" title="Per
 <p>The tools included here are the most widely used and well maintained among AS event detection tools. If you would like to include your tool in the pipeline please let us know.
 We hope this collection can be a starting point for future benchmarking approaches and quality control.</p>
 <figure class="align-default">
-<img alt="_images/Screenshot_dicast.png" src="_images/Screenshot_dicast.png" />
+<img alt="_images/pipeline.png" src="_images/pipeline.png" />
 </figure>
 </section>
 <section id="what-is-dicast">

diff --git a/docs/build/html/further-information/about.html b/docs/build/html/further-information/about.html
@@ -67,13 +67,13 @@
 </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">
+<li class="toctree-l2"><a class="reference internal" href="../get-started/run/dicast-cli.html">Run DICAST via Command Line 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 (depreciated)</a><ul class="simple">
+<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">
 </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">
+<li class="toctree-l2"><a class="reference internal" href="../get-started/run/gui.html">Run DICAST with a graphical user interface (depreciated)</a><ul class="simple">
 </ul>
 </li>
 <li class="toctree-l2"><a class="reference internal" href="../get-started/run/outputs.html">DICAST Outputs</a></li>

diff --git a/docs/build/html/further-information/example-files.html b/docs/build/html/further-information/example-files.html
@@ -68,13 +68,13 @@
 </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">
+<li class="toctree-l2"><a class="reference internal" href="../get-started/run/dicast-cli.html">Run DICAST via Command Line 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 (depreciated)</a><ul class="simple">
+<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">
 </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">
+<li class="toctree-l2"><a class="reference internal" href="../get-started/run/gui.html">Run DICAST with a graphical user interface (depreciated)</a><ul class="simple">
 </ul>
 </li>
 <li class="toctree-l2"><a class="reference internal" href="../get-started/run/outputs.html">DICAST Outputs</a></li>
@@ -176,13 +176,13 @@ <h2>Running multiple mapping tools (E.g., STAR, HISAT2 and bbmap)<a class="heade
 <li><p>Download or copy the genome fasta file into the <cite>input</cite> folder. Dont’t forget to uncompress it. E.g.:</p></li>
 </ol>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span class="prompt1"><span class="nb">cd</span> /path/to/DICAST/input</span>
-<span class="prompt1">wget http://ftp.ensembl.org/pub/release-104/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz</span>
+<span class="prompt1">wget http://ftp.ensembl.org/pub/release-105/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz</span>
 <span class="prompt1">gunzip Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz</span>
 </pre></div></div><ol class="arabic simple" start="6">
 <li><p>Download or copy the genome gtf annotation into the <cite>input</cite> folder. Dont’t forget to uncompress it. E.g.:</p></li>
 </ol>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span class="prompt1">wget http://ftp.ensembl.org/pub/release-104/gtf/homo_sapiens/Homo_sapiens.GRCh38.104.gtf.gz</span>
-<span class="prompt1">gunzip Homo_sapiens.GRCh38.104.gtf.gz</span>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span class="prompt1">wget http://ftp.ensembl.org/pub/release-105/gtf/homo_sapiens/Homo_sapiens.GRCh38.105.gtf.gz</span>
+<span class="prompt1">gunzip Homo_sapiens.GRCh38.105.gtf.gz</span>
 </pre></div></div><ol class="arabic simple" start="7">
 <li><p>Download or copy the fastq files you want to align into the <cite>/path/to/DICAST/input/controldir/fastqdir</cite>. Note: we support only paired-end RNA-Seq - fastq files have to be in pairs.</p></li>
 <li><p>Go to <cite>/path/to/DICAST/scripts</cite> and edit <cite>config.sh</cite> according to your run (see <a class="reference internal" href="../get-started/config/general_parameters.html"><span class="doc">How to change your config.sh file</span></a>):</p></li>
@@ -196,7 +196,7 @@ <h2>Running multiple mapping tools (E.g., STAR, HISAT2 and bbmap)<a class="heade
 }
 </style><span class="prompt2">read_length=76</span>
 <span class="prompt2">fastaname=Homo_sapiens.GRCh38.dna.primary_assembly.fa</span>
-<span class="prompt2">gtfname=Homo_sapiens.GRCh38.104.gtf</span>
+<span class="prompt2">gtfname=Homo_sapiens.GRCh38.105.gtf</span>
 </pre></div></div><ol class="arabic simple" start="9">
 <li><p>List the mapping tools you want to run:</p></li>
 </ol>
@@ -236,18 +236,18 @@ <h2>Running multiple alternative splicing event detection tools (E.g., MAJIQ and
 <li><p>Download or copy the genome fasta file into the <cite>input</cite> folder. Dont’t forget to uncompress it. E.g.:</p></li>
 </ol>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span class="prompt1"><span class="nb">cd</span> /path/to/DICAST/input</span>
-<span class="prompt1">wget http://ftp.ensembl.org/pub/release-104/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz</span>
+<span class="prompt1">wget http://ftp.ensembl.org/pub/release-105/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz</span>
 <span class="prompt1">gunzip Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz</span>
 </pre></div></div><ol class="arabic simple" start="6">
 <li><p>Download or copy the genome annotation file into the <cite>input</cite> folder. Dont’t forget to uncompress it. E.g.:</p></li>
 </ol>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span class="prompt1">wget http://ftp.ensembl.org/pub/release-104/gtf/homo_sapiens/Homo_sapiens.GRCh38.104.gtf.gz</span>
-<span class="prompt1">gunzip Homo_sapiens.GRCh38.104.gtf.gz</span>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span class="prompt1">wget http://ftp.ensembl.org/pub/release-105/gtf/homo_sapiens/Homo_sapiens.GRCh38.105.gtf.gz</span>
+<span class="prompt1">gunzip Homo_sapiens.GRCh38.105.gtf.gz</span>
 </pre></div></div><ol class="arabic simple" start="7">
 <li><p>Download or copy the genome gff3 annotation into the <cite>input</cite> folder (for MAJIQ). Dont’t forget to uncompress it. E.g.:</p></li>
 </ol>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span class="prompt1">wget http://ftp.ensembl.org/pub/release-104/gff3/homo_sapiens/Homo_sapiens.GRCh38.104.gff3.gz</span>
-<span class="prompt1">gunzip Homo_sapiens.GRCh38.104.gff3.gz</span>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span class="prompt1">wget http://ftp.ensembl.org/pub/release-105/gff3/homo_sapiens/Homo_sapiens.GRCh38.105.gff3.gz</span>
+<span class="prompt1">gunzip Homo_sapiens.GRCh38.105.gff3.gz</span>
 </pre></div></div><ol class="arabic simple" start="8">
 <li><p>Download or copy the fastq files you want to use into the <cite>/path/to/DICAST/input/controldir/fastqdir</cite>. Note: we support only paired-end RNA-Seq - fastq files have to be in pairs.</p></li>
 <li><p>Download or copy the bam files you want to use into the <cite>/path/to/DICAST/input/controldir/bamdir</cite>.</p></li>
@@ -258,8 +258,8 @@ <h2>Running multiple alternative splicing event detection tools (E.g., MAJIQ and
 </pre></div></div><p>In the <cite>config.sh</cite> file edit the following lines:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span class="prompt1"><span class="nv">read_length</span><span class="o">=</span><span class="m">76</span></span>
 <span class="prompt1"><span class="nv">fastaname</span><span class="o">=</span>Homo_sapiens.GRCh38.dna.primary_assembly.fa</span>
-<span class="prompt1"><span class="nv">gtfname</span><span class="o">=</span>Homo_sapiens.GRCh38.104.gtf</span>
-<span class="prompt1"><span class="nv">gffname</span><span class="o">=</span>Homo_sapiens.GRCh38.104.gff3</span>
+<span class="prompt1"><span class="nv">gtfname</span><span class="o">=</span>Homo_sapiens.GRCh38.105.gtf</span>
+<span class="prompt1"><span class="nv">gffname</span><span class="o">=</span>Homo_sapiens.GRCh38.105.gff3</span>
 </pre></div></div><ol class="arabic simple" start="11">
 <li><p>List the mapping tools you want to run:</p></li>
 </ol>

diff --git a/docs/build/html/further-information/faq.html b/docs/build/html/further-information/faq.html
@@ -68,13 +68,13 @@
 </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">
+<li class="toctree-l2"><a class="reference internal" href="../get-started/run/dicast-cli.html">Run DICAST via Command Line 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 (depreciated)</a><ul class="simple">
+<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">
 </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">
+<li class="toctree-l2"><a class="reference internal" href="../get-started/run/gui.html">Run DICAST with a graphical user interface (depreciated)</a><ul class="simple">
 </ul>
 </li>
 <li class="toctree-l2"><a class="reference internal" href="../get-started/run/outputs.html">DICAST Outputs</a></li>