SCHWED-4563: clarified Singularity setup and added example.

doc/container/singularity.rst

@@ -36,6 +36,8 @@ Fire the local Registry and push the promod image to it:
   sudo docker tag promod localhost:5000/promod
   sudo docker push localhost:5000/promod
 
+If port 5000 is already taken on your machine, use a different ``<PORT>`` by
+using the flag ``-p <PORT>:5000`` and ``localhost:<PORT>`` in these commands.
 Make sure, that on top of your Singularity recipe you have something like:
 
 .. code-block:: bash
@@ -71,7 +73,24 @@ To get help on how to run it:
 
 .. code-block:: bash
 
-  singularity run --app Notebook <IMAGE> --help
+  singularity help --app Notebook <IMAGE>
+
+Within the notebook you can test OST, ProMod3 and nglview as follows:
+
+.. code-block:: python
+
+  from ost import io
+  from promod3 import loop
+  import nglview
+
+  # generate backbone with dihedrals of a helix and store it
+  sequence = "HELLYEAH"
+  bb_list = loop.BackboneList(sequence)
+  io.SavePDB(bb_list.ToEntity(), "test.pdb")
+
+  # display stored file
+  view = nglview.show_file("test.pdb")
+  view
 
 
 The Compound Library

doc/html/_sources/container/singularity.txt

@@ -36,6 +36,8 @@ Fire the local Registry and push the promod image to it:
   sudo docker tag promod localhost:5000/promod
   sudo docker push localhost:5000/promod
 
+If port 5000 is already taken on your machine, use a different ``<PORT>`` by
+using the flag ``-p <PORT>:5000`` and ``localhost:<PORT>`` in these commands.
 Make sure, that on top of your Singularity recipe you have something like:
 
 .. code-block:: bash
@@ -71,7 +73,24 @@ To get help on how to run it:
 
 .. code-block:: bash
 
-  singularity run --app Notebook <IMAGE> --help
+  singularity help --app Notebook <IMAGE>
+
+Within the notebook you can test OST, ProMod3 and nglview as follows:
+
+.. code-block:: python
+
+  from ost import io
+  from promod3 import loop
+  import nglview
+
+  # generate backbone with dihedrals of a helix and store it
+  sequence = "HELLYEAH"
+  bb_list = loop.BackboneList(sequence)
+  io.SavePDB(bb_list.ToEntity(), "test.pdb")
+
+  # display stored file
+  view = nglview.show_file("test.pdb")
+  view
 
 
 The Compound Library

doc/html/container/singularity.html

@@ -57,7 +57,9 @@ sudo docker tag promod localhost:5000/promod
 sudo docker push localhost:5000/promod
 </pre></div>
 </div>
-<p>Make sure, that on top of your Singularity recipe you have something like:</p>
+<p>If port 5000 is already taken on your machine, use a different <code class="docutils literal"><span class="pre">&lt;PORT&gt;</span></code> by
+using the flag <code class="docutils literal"><span class="pre">-p</span> <span class="pre">&lt;PORT&gt;:5000</span></code> and <code class="docutils literal"><span class="pre">localhost:&lt;PORT&gt;</span></code> in these commands.
+Make sure, that on top of your Singularity recipe you have something like:</p>
 <div class="highlight-bash"><div class="highlight"><pre><span></span>BootStrap: docker
 Registry: http://localhost:5000
 Namespace:
@@ -81,7 +83,22 @@ E.g. to run scripts with pm:</p>
 </div>
 <p>The jupyter notebook is setup as an app in the container.
 To get help on how to run it:</p>
-<div class="highlight-bash"><div class="highlight"><pre><span></span>singularity run --app Notebook &lt;IMAGE&gt; --help
+<div class="highlight-bash"><div class="highlight"><pre><span></span>singularity <span class="nb">help</span> --app Notebook &lt;IMAGE&gt;
+</pre></div>
+</div>
+<p>Within the notebook you can test OST, ProMod3 and nglview as follows:</p>
+<div class="highlight-python"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">loop</span>
+<span class="kn">import</span> <span class="nn">nglview</span>
+
+<span class="c1"># generate backbone with dihedrals of a helix and store it</span>
+<span class="n">sequence</span> <span class="o">=</span> <span class="s2">&quot;HELLYEAH&quot;</span>
+<span class="n">bb_list</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">BackboneList</span><span class="p">(</span><span class="n">sequence</span><span class="p">)</span>
+<span class="n">io</span><span class="o">.</span><span class="n">SavePDB</span><span class="p">(</span><span class="n">bb_list</span><span class="o">.</span><span class="n">ToEntity</span><span class="p">(),</span> <span class="s2">&quot;test.pdb&quot;</span><span class="p">)</span>
+
+<span class="c1"># display stored file</span>
+<span class="n">view</span> <span class="o">=</span> <span class="n">nglview</span><span class="o">.</span><span class="n">show_file</span><span class="p">(</span><span class="s2">&quot;test.pdb&quot;</span><span class="p">)</span>
+<span class="n">view</span>
 </pre></div>
 </div>
 </div>