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 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-generic">generic</a></li>
179 <li><a href="#section-arvados">arvados</a></li>
182 <section id="section-generic">{{ generic_tab_content | markdownify}}</section>
183 <section id="section-arvados">{{ arvados_tab_content | markdownify}}</section>
186 {% include links.md %}