Add changes for df98ebb

_sources/docker.rst.txt

@@ -301,23 +301,3 @@ Syntax: **\--volume/-v** *host:container*
   > ls -l /scratch
   > exit
 
-
-Volume exercises
-================
-
-1. Copy the 2 fastq files from available datasets in Github repository and place them in mounted directory
-
-2. Run fastqc interactively (inside container): ```fastqc  /scratch/*.gz```
-
-3. Run fastqc non-interactively (outside the container)
-
-docker run \--user
------------------
-
-It is possible to run some containers with a specific user, appending ```run --user```.
-
-A convenient command would be:
-
-.. code-block:: console
-
-  docker run --user $(id -u):$(id -g) --detach --volume $(pwd)/test:/scratch --name user_test biocontainers/fastqc:v0.11.9_cv7 touch /scratch/userfile

docker.html

@@ -69,10 +69,6 @@
 </ul>
 </li>
 <li class="toctree-l2"><a class="reference internal" href="#volumes">Volumes</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#volume-exercises">Volume exercises</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="#docker-run-user">docker run --user</a></li>
-</ul>
-</li>
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="docker_2.html">Docker 2</a></li>
@@ -313,22 +309,6 @@ <h2>Volumes<a class="headerlink" href="#volumes" title="Link to this heading">
 </pre></div>
 </div>
 </section>
-<section id="volume-exercises">
-<h2>Volume exercises<a class="headerlink" href="#volume-exercises" title="Link to this heading"></a></h2>
-<ol class="arabic simple">
-<li><p>Copy the 2 fastq files from available datasets in Github repository and place them in mounted directory</p></li>
-<li><p>Run fastqc interactively (inside container): <code class="docutils literal notranslate"><span class="pre">`fastqc</span>&#160; <span class="pre">/scratch/*.gz`</span></code></p></li>
-<li><p>Run fastqc non-interactively (outside the container)</p></li>
-</ol>
-<section id="docker-run-user">
-<h3>docker run --user<a class="headerlink" href="#docker-run-user" title="Link to this heading"></a></h3>
-<p>It is possible to run some containers with a specific user, appending <code class="docutils literal notranslate"><span class="pre">`run</span> <span class="pre">--user`</span></code>.</p>
-<p>A convenient command would be:</p>
-<div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="go">docker run --user $(id -u):$(id -g) --detach --volume $(pwd)/test:/scratch --name user_test biocontainers/fastqc:v0.11.9_cv7 touch /scratch/userfile</span>
-</pre></div>
-</div>
-</section>
-</section>
 </section>