Note: if you don't have example sequence data or the STAR index files, see [setup](/setup.html).
-{% assign tabs = "generic, arvados" | split: ", " %}
-{% capture generic_tab_content %}
+{% capture generic_input_tab_content %}
main-input.yaml
```
fq:
{: .challenge }
{% endcapture %}
-{% capture arvados_tab_content %}
+{% capture arvados_input_tab_content %}
main-input.yaml
```
fq:
<div class="tabbed">
<ul class="tab">
- {% for tab in tabs %}
- <li><a href="#section-{{ tab }}">{{ tab }}</a></li>
- {% endfor %}
+ <li><a href="#section-generic-input">generic</a></li>
+ <li><a href="#section-arvados-input">arvados</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-input">{{ generic_input_tab_content | markdownify}}</section>
+ <section id="section-arvados-input">{{ arvados_input_tab_content | markdownify}}</section>
</div>
# Debugging the workflow
The CWL runner will print a results JSON object to standard output. It will look something like this (it may include additional fields).
-<div>
-{% tabs output %}
+{% capture generic_output_tab_content %}
-{% tab output generic %}
```
{
"bam_sorted_indexed": {
}
```
{: .language-yaml }
-{% endtab %}
+{% endcapture %}
-{% tab output arvados %}
+{% capture arvados_output_tab_content %}
```
{
"bam_sorted_indexed": {
}
```
{: .language-yaml }
-{% endtab %}
-{% endtabs %}
+{% endcapture %}
+
+<div class="tabbed">
+ <ul class="tab">
+ <li><a href="#section-generic-output">generic</a></li>
+ <li><a href="#section-arvados-output">arvados</a></li>
+ </ul>
+
+ <section id="section-generic-output">{{ generic_output_tab_content | markdownify}}</section>
+ <section id="section-arvados-output">{{ arvados_output_tab_content | markdownify}}</section>
</div>
This has a similar structure as `main-input.yaml`. The each output
parameter is listed, with the `location` field of each `File` object
indicating where the output file can be found.
-
window.addEventListener('load', function() {
// Get relevant elements and collections
- const tabbed = document.querySelector('.tabbed');
+ const allTabbed = document.querySelectorAll('.tabbed');
+
+ allTabbed.forEach((tabbed) => {
+
const tablist = tabbed.querySelector('ul');
const tabs = tablist.querySelectorAll('a');
const panels = tabbed.querySelectorAll('[id^="section"]');
tabs[0].setAttribute('aria-selected', 'true');
tabs[0].setAttribute('class', 'active');
panels[0].hidden = false;
-});
+ });
+}
+);
title: Setup
---
-<div>
-{% tabs setup %}
-{% tab setup generic %}
+{% capture generic_tab_content %}
# Setting up a practice repository
```
{: .language-bash }
+{% endcapture %}
-{% endtab %}
-
-{% tab setup arvados %}
+{% capture arvados_tab_content %}
# Setting up a practice repository
We will create a new git repository and import a library of existing
tool definitions that will help us build our workflow.
-When using the recommended VSCode environment to develop on Arvados, start by forking this repository:
-```
-git clone https://github.com/arvados/arvados-vscode-cwl-template.git rnaseq-cwl-training-exercises
-```
-{: .language-bash }
+When using the recommended [VSCode environment to develop on Arvados](https://doc.arvados.org/v2.3/user/cwl/arvados-vscode-training.html),
+start by forking the
+[arvados-vscode-cwl-template](https://github.com/arvados/arvados-vscode-cwl-template)
+repository.
-Next, import bio-cwl-tools with this command:
+1. Vscode: On the left sidebar, choose `Explorer` 
+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`
+Next, import the [bio-cwl-tools](https://github.com/common-workflow-library/bio-cwl-tools) repository:
+
+1. Vscode: In the top menu, select `Terminal` → `New Terminal`
+1. This will open a terminal window in the lower part of the screen
+1. Run this command:
```
git submodule add https://github.com/common-workflow-library/bio-cwl-tools.git
```
> you do not need to perform this download step.
{: .callout}
-Use `arv-copy` to copy the collection:
+1. Go to 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).
+
+Now, on shell node of your Arvados cluster, use `arv-copy` to copy the collection:
```
arv-copy --src jutro 9178fe1b80a08a422dbe02adfd439764+925
```
{: .language-bash }
-## Sneak peak
-If you want to jump ahead, here are links to some of the CWL concepts you just used
- - [YAML array] (https://www.commonwl.org/user_guide/yaml/#arrays)
- - [CWL array inputs] (https://www.commonwl.org/user_guide/09-array-inputs/index.html)
-
-{% endtab %}
-{% endtabs %}
+{% endcapture %}
+
+<div class="tabbed">
+ <ul class="tab">
+ <li><a href="#section-generic">generic</a></li>
+ <li><a href="#section-arvados">arvados</a></li>
+ </ul>
+
+ <section id="section-generic">{{ generic_tab_content | markdownify}}</section>
+ <section id="section-arvados">{{ arvados_tab_content | markdownify}}</section>
</div>
{% include links.md %}
projects / rnaseq-cwl-training.git / commitdiff
