Remove software carpentries logo

[rnaseq-cwl-training.git] / setup.md

diff --git a/setup.md b/setup.md
index 8a30e9198137422d3f7831712c8a01a7e14265c6..358a1ccee96e2f409d0c67863de6a94a5f442962 100644 (file)
--- a/setup.md
+++ b/setup.md
@@ -87,7 +87,7 @@ start by forking the
 [arvados-vscode-cwl-template](https://github.com/arvados/arvados-vscode-cwl-template)
 repository.
 
-1. Vscode: On the left sidebar, choose `Explorer` ![](../assets/img/Explorer.png)
+1. Vscode: On the left sidebar, choose `Explorer` ![](assets/img/Explorer.png)
 1. Select `Clone Repository` and enter [https://github.com/arvados/arvados-vscode-cwl-template](https://github.com/arvados/arvados-vscode-cwl-template), then click `Open`
 1. If asked `Would you like to open the cloned repository?` choose `Open`
 
@@ -113,10 +113,10 @@ git submodule add https://github.com/common-workflow-library/bio-cwl-tools.git
 > you do not need to perform this download step.
 {: .callout}
 
-1. Go to https://workbench2.jutro.arvadosapi.com and sign in, this will create an account
+1. Go to [https://workbench2.jutro.arvadosapi.com](https://workbench2.jutro.arvadosapi.com) and sign in, this will create an account
 2. Go to `Get an API token` under the user menu
 3. Log into the shell node of your Arvados cluster
-4. On the shell node, copy the host name and token for the 'jutro' cluster into the file `~/.config/arvados/jutro.conf` as described on the page for [arv-copy](https://doc.arvados.org/user/topics/arv-copy.html).
+4. On the shell node, copy the host name and token for the `jutro` cluster into the file `~/.config/arvados/jutro.conf` as described on the page for [arv-copy](https://doc.arvados.org/user/topics/arv-copy.html).
 
 Now, on shell node of your Arvados cluster, use `arv-copy` to copy the collection:
 
@@ -175,12 +175,12 @@ arvados-cwl-runner bio-cwl-tools/STAR/STAR-Index.cwl chr1-star-index.yaml
 
 <div class="tabbed">
   <ul class="tab">
-      <li><a href="#section-generic">generic</a></li>
       <li><a href="#section-arvados">arvados</a></li>
+      <li><a href="#section-generic">generic</a></li>
   </ul>
 
-  <section id="section-generic">{{ generic_tab_content | markdownify}}</section>
   <section id="section-arvados">{{ arvados_tab_content | markdownify}}</section>
+  <section id="section-generic">{{ generic_tab_content | markdownify}}</section>
 </div>
 
 {% include links.md %}