Added links to YAML and CWL array

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

diff --git a/setup.md b/setup.md
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--- a/setup.md
+++ b/setup.md
@@ -1,7 +1,175 @@
 ---
 title: Setup
 ---
-FIXME
 
+<div>
+{% tabs setup %}
+{% tab setup generic %}
+
+# 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 }
+
+
+{% endtab %}
+
+{% tab setup arvados %}
+
+# 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 }
+
+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
+
+> ## 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}
+
+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 }
+
+## 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 %}
+</div>
 
 {% include links.md %}