X-Git-Url: https://git.arvados.org/rnaseq-cwl-training.git/blobdiff_plain/9126e9209dec22eae0093204c060cbe4c139f720..HEAD:/setup.md

diff --git a/setup.md b/setup.md
index f907ec7..358a1cc 100644
--- a/setup.md
+++ b/setup.md
@@ -2,28 +2,26 @@
 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 git repository to hold our workflow with this command:
+Create a new empty git repository to hold our workflow with this command:
 
 ```
 git init rnaseq-cwl-training-exercises
 ```
-
-On Arvados use this:
-
-```
-git clone https://github.com/arvados/arvados-vscode-cwl-template.git 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
 
@@ -32,8 +30,9 @@ Start from your rnaseq-cwl-exercises directory.
 ```
 mkdir rnaseq
 cd rnaseq
-wget --mirror --no-parent --no-host --cut-dirs=1 https://download.pirca.arvadosapi.com/c=9178fe1b80a08a422dbe02adfd439764+925/
+wget --mirror --no-parent --no-host --cut-dirs=1 https://download.jutro.arvadosapi.com/c=9178fe1b80a08a422dbe02adfd439764+925/
 ```
+{: .language-bash }
 
 # Downloading or generating STAR index
 
@@ -46,8 +45,9 @@ This is a rather large download (4 GB).  Depending on your bandwidth, it may be
 ```
 mkdir hg19-chr1-STAR-index
 cd hg19-chr1-STAR-index
-wget --mirror --no-parent --no-host --cut-dirs=1 https://download.pirca.arvadosapi.com/c=02a12ce9e2707610991bd29d38796b57+2912/
+wget --mirror --no-parent --no-host --cut-dirs=1 https://download.jutro.arvadosapi.com/c=02a12ce9e2707610991bd29d38796b57+2912/
 ```
+{: .language-bash }
 
 ## Generating
 
@@ -64,12 +64,123 @@ Gtf:
   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](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-arvados">arvados</a></li>
+      <li><a href="#section-generic">generic</a></li>
+  </ul>
 
+  <section id="section-arvados">{{ arvados_tab_content | markdownify}}</section>
+  <section id="section-generic">{{ generic_tab_content | markdownify}}</section>
+</div>
 
 {% include links.md %}