7 {% tab setup generic %}
9 # Setting up a practice repository
11 We will create a new git repository and import a library of existing
12 tool definitions that will help us build our workflow.
14 Create a new empty git repository to hold our workflow with this command:
17 git init rnaseq-cwl-training-exercises
21 Next, import bio-cwl-tools with this command:
24 git submodule add https://github.com/common-workflow-library/bio-cwl-tools.git
28 # Downloading sample and reference data
30 Start from your rnaseq-cwl-exercises directory.
35 wget --mirror --no-parent --no-host --cut-dirs=1 https://download.jutro.arvadosapi.com/c=9178fe1b80a08a422dbe02adfd439764+925/
39 # Downloading or generating STAR index
41 Running STAR requires index files generated from the reference.
43 This is a rather large download (4 GB). Depending on your bandwidth, it may be faster to generate it yourself.
48 mkdir hg19-chr1-STAR-index
49 cd hg19-chr1-STAR-index
50 wget --mirror --no-parent --no-host --cut-dirs=1 https://download.jutro.arvadosapi.com/c=02a12ce9e2707610991bd29d38796b57+2912/
56 Create `chr1-star-index.yaml`:
61 location: rnaseq/reference_data/chr1.fa
62 format: http://edamontology.org/format_1930
63 IndexName: 'hg19-chr1-STAR-index'
66 location: rnaseq/reference_data/chr1-hg19_genes.gtf
71 Generate the index with your local cwl-runner.
74 cwl-runner bio-cwl-tools/STAR/STAR-Index.cwl chr1-star-index.yaml
81 {% tab setup arvados %}
83 # Setting up a practice repository
85 We will create a new git repository and import a library of existing
86 tool definitions that will help us build our workflow.
88 When using the recommended VSCode environment to develop on Arvados, start by forking this repository:
90 git clone https://github.com/arvados/arvados-vscode-cwl-template.git rnaseq-cwl-training-exercises
94 Next, import bio-cwl-tools with this command:
97 git submodule add https://github.com/common-workflow-library/bio-cwl-tools.git
101 # Downloading sample and reference data
105 > You may already have access to this collection.
107 > You can check by going to Workbench and pasting
108 > `9178fe1b80a08a422dbe02adfd439764+925` into the search box. If you
109 > arrived at a collection page instead of a "not found" error, then
110 > you do not need to perform this download step.
113 Use `arv-copy` to copy the collection:
116 arv-copy --src jutro 9178fe1b80a08a422dbe02adfd439764+925
120 # Downloading or generating STAR index
122 Running STAR requires index files generated from the reference.
124 This is a rather large download (4 GB). Depending on your bandwidth, it may be faster to generate it yourself.
130 > As above, you can check by going to Workbench and pasting
131 > `02a12ce9e2707610991bd29d38796b57+2912` into the search box to see
132 > if you already have access to this collection.
135 Use `arv-copy` to copy the collection:
138 arv-copy --src jutro 02a12ce9e2707610991bd29d38796b57+2912
144 Create `chr1-star-index.yaml`:
149 location: keep:9178fe1b80a08a422dbe02adfd439764+925/reference_data/chr1.fa
150 format: http://edamontology.org/format_1930
151 IndexName: 'hg19-chr1-STAR-index'
154 location: keep:9178fe1b80a08a422dbe02adfd439764+925/reference_data/chr1-hg19_genes.gtf
159 Generate the index with arvados-cwl-runner.
162 arvados-cwl-runner bio-cwl-tools/STAR/STAR-Index.cwl chr1-star-index.yaml
170 {% include links.md %}