---
title: Setup
---

{% capture generic_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.

Create a new empty git repository to hold our workflow with this command:

```
git init rnaseq-cwl-training-exercises
```
{: .language-bash }

Next, import bio-cwl-tools with this command:

```
git submodule add https://github.com/common-workflow-library/bio-cwl-tools.git
```
{: .language-bash }

# Downloading sample and reference data

Start from your rnaseq-cwl-exercises directory.

```
mkdir rnaseq
cd rnaseq
wget --mirror --no-parent --no-host --cut-dirs=1 https://download.jutro.arvadosapi.com/c=9178fe1b80a08a422dbe02adfd439764+925/
```
{: .language-bash }

# Downloading or generating STAR index

Running STAR requires index files generated from the reference.

This is a rather large download (4 GB).  Depending on your bandwidth, it may be faster to generate it yourself.

## Downloading

```
mkdir hg19-chr1-STAR-index
cd hg19-chr1-STAR-index
wget --mirror --no-parent --no-host --cut-dirs=1 https://download.jutro.arvadosapi.com/c=02a12ce9e2707610991bd29d38796b57+2912/
```
{: .language-bash }

## Generating

Create `chr1-star-index.yaml`:

```
InputFiles:
  - class: File
    location: rnaseq/reference_data/chr1.fa
    format: http://edamontology.org/format_1930
IndexName: 'hg19-chr1-STAR-index'
Gtf:
  class: File
  location: rnaseq/reference_data/chr1-hg19_genes.gtf
Overhang: 99
```
{: .language-yaml }

Generate the index with your local cwl-runner.

```
cwl-runner bio-cwl-tools/STAR/STAR-Index.cwl chr1-star-index.yaml
```
{: .language-bash }

{% endcapture %}

{% 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](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.

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`

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
```
{: .language-bash }

# Downloading sample and reference data

> ## Note
>
> You may already have access to this collection.
>
> You can check by going to Workbench and pasting
> `9178fe1b80a08a422dbe02adfd439764+925` into the search box.  If you
> arrived at a collection page instead of a "not found" error, then
> 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
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 }

# Downloading or generating STAR index

Running STAR requires index files generated from the reference.

This is a rather large download (4 GB).  Depending on your bandwidth, it may be faster to generate it yourself.

## Downloading

> ## Note
>
> As above, you can check by going to Workbench and pasting
> `02a12ce9e2707610991bd29d38796b57+2912` into the search box to see
> if you already have access to this collection.
{: .callout}

Use `arv-copy` to copy the collection:

```
arv-copy --src jutro 02a12ce9e2707610991bd29d38796b57+2912
```
{: .language-bash }

## Generating

Create `chr1-star-index.yaml`:

```
InputFiles:
  - class: File
    location: keep:9178fe1b80a08a422dbe02adfd439764+925/reference_data/chr1.fa
    format: http://edamontology.org/format_1930
IndexName: 'hg19-chr1-STAR-index'
Gtf:
  class: File
  location: keep:9178fe1b80a08a422dbe02adfd439764+925/reference_data/chr1-hg19_genes.gtf
Overhang: 99
```
{: .language-yaml }

Generate the index with arvados-cwl-runner.

```
arvados-cwl-runner bio-cwl-tools/STAR/STAR-Index.cwl chr1-star-index.yaml
```
{: .language-bash }

{% 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 %}