5 {% capture generic_tab_content %}
7 # Setting up a practice repository
9 We will create a new git repository and import a library of existing
10 tool definitions that will help us build our workflow.
12 Create a new empty git repository to hold our workflow with this command:
15 git init rnaseq-cwl-training-exercises
19 Next, import bio-cwl-tools with this command:
22 git submodule add https://github.com/common-workflow-library/bio-cwl-tools.git
26 # Downloading sample and reference data
28 Start from your rnaseq-cwl-exercises directory.
33 wget --mirror --no-parent --no-host --cut-dirs=1 https://download.jutro.arvadosapi.com/c=9178fe1b80a08a422dbe02adfd439764+925/
37 # Downloading or generating STAR index
39 Running STAR requires index files generated from the reference.
41 This is a rather large download (4 GB). Depending on your bandwidth, it may be faster to generate it yourself.
46 mkdir hg19-chr1-STAR-index
47 cd hg19-chr1-STAR-index
48 wget --mirror --no-parent --no-host --cut-dirs=1 https://download.jutro.arvadosapi.com/c=02a12ce9e2707610991bd29d38796b57+2912/
54 Create `chr1-star-index.yaml`:
59 location: rnaseq/reference_data/chr1.fa
60 format: http://edamontology.org/format_1930
61 IndexName: 'hg19-chr1-STAR-index'
64 location: rnaseq/reference_data/chr1-hg19_genes.gtf
69 Generate the index with your local cwl-runner.
72 cwl-runner bio-cwl-tools/STAR/STAR-Index.cwl chr1-star-index.yaml
78 {% capture arvados_tab_content %}
80 # Setting up a practice repository
82 We will create a new git repository and import a library of existing
83 tool definitions that will help us build our workflow.
85 When using the recommended [VSCode environment to develop on Arvados](https://doc.arvados.org/v2.3/user/cwl/arvados-vscode-training.html),
87 [arvados-vscode-cwl-template](https://github.com/arvados/arvados-vscode-cwl-template)
90 1. Vscode: On the left sidebar, choose `Explorer` ![](assets/img/Explorer.png)
91 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`
92 1. If asked `Would you like to open the cloned repository?` choose `Open`
94 Next, import the [bio-cwl-tools](https://github.com/common-workflow-library/bio-cwl-tools) repository:
96 1. Vscode: In the top menu, select `Terminal` → `New Terminal`
97 1. This will open a terminal window in the lower part of the screen
100 git submodule add https://github.com/common-workflow-library/bio-cwl-tools.git
104 # Downloading sample and reference data
108 > You may already have access to this collection.
110 > You can check by going to Workbench and pasting
111 > `9178fe1b80a08a422dbe02adfd439764+925` into the search box. If you
112 > arrived at a collection page instead of a "not found" error, then
113 > you do not need to perform this download step.
116 1. Go to [https://workbench2.jutro.arvadosapi.com](https://workbench2.jutro.arvadosapi.com) and sign in, this will create an account
117 2. Go to `Get an API token` under the user menu
118 3. Log into the shell node of your Arvados cluster
119 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).
121 Now, on shell node of your Arvados cluster, use `arv-copy` to copy the collection:
124 arv-copy --src jutro 9178fe1b80a08a422dbe02adfd439764+925
128 # Downloading or generating STAR index
130 Running STAR requires index files generated from the reference.
132 This is a rather large download (4 GB). Depending on your bandwidth, it may be faster to generate it yourself.
138 > As above, you can check by going to Workbench and pasting
139 > `02a12ce9e2707610991bd29d38796b57+2912` into the search box to see
140 > if you already have access to this collection.
143 Use `arv-copy` to copy the collection:
146 arv-copy --src jutro 02a12ce9e2707610991bd29d38796b57+2912
152 Create `chr1-star-index.yaml`:
157 location: keep:9178fe1b80a08a422dbe02adfd439764+925/reference_data/chr1.fa
158 format: http://edamontology.org/format_1930
159 IndexName: 'hg19-chr1-STAR-index'
162 location: keep:9178fe1b80a08a422dbe02adfd439764+925/reference_data/chr1-hg19_genes.gtf
167 Generate the index with arvados-cwl-runner.
170 arvados-cwl-runner bio-cwl-tools/STAR/STAR-Index.cwl chr1-star-index.yaml
178 <li><a href="#section-arvados">arvados</a></li>
179 <li><a href="#section-generic">generic</a></li>
182 <section id="section-arvados">{{ arvados_tab_content | markdownify}}</section>
183 <section id="section-generic">{{ generic_tab_content | markdownify}}</section>
186 {% include links.md %}