setup.md

   1 ---
   2 title: Setup
   3 ---
   4
   5 # Setting up a practice repository
   6
   7 We will create a new git repository and import a library of existing
   8 tool definitions that will help us build our workflow.
   9
  10 Create a new git repository to hold our workflow with this command:
  11
  12 ```
  13 git init rnaseq-cwl-training-exercises
  14 ```
  15
  16 On Arvados use this:
  17
  18 ```
  19 git clone https://github.com/arvados/arvados-vscode-cwl-template.git rnaseq-cwl-training-exercises
  20 ```
  21
  22 Next, import bio-cwl-tools with this command:
  23
  24 ```
  25 git submodule add https://github.com/common-workflow-library/bio-cwl-tools.git
  26 ```
  27
  28 # Downloading sample and reference data
  29
  30 Start from your rnaseq-cwl-exercises directory.
  31
  32 ```
  33 mkdir rnaseq
  34 cd rnaseq
  35 wget --mirror --no-parent --no-host --cut-dirs=1 https://download.pirca.arvadosapi.com/c=9178fe1b80a08a422dbe02adfd439764+925/
  36 ```
  37
  38 # Downloading or generating STAR index
  39
  40 Running STAR requires index files generated from the reference.
  41
  42 This is a rather large download (4 GB).  Depending on your bandwidth, it may be faster to generate it yourself.
  43
  44 ## Downloading
  45
  46 ```
  47 mkdir hg19-chr1-STAR-index
  48 cd hg19-chr1-STAR-index
  49 wget --mirror --no-parent --no-host --cut-dirs=1 https://download.pirca.arvadosapi.com/c=02a12ce9e2707610991bd29d38796b57+2912/
  50 ```
  51
  52 ## Generating
  53
  54 Create `chr1-star-index.yaml`:
  55
  56 ```
  57 InputFiles:
  58   - class: File
  59     location: rnaseq/reference_data/chr1.fa
  60     format: http://edamontology.org/format_1930
  61 IndexName: 'hg19-chr1-STAR-index'
  62 Gtf:
  63   class: File
  64   location: rnaseq/reference_data/chr1-hg19_genes.gtf
  65 Overhang: 99
  66 ```
  67
  68 Generate the index with your local cwl-runner.
  69
  70 ```
  71 cwl-runner bio-cwl-tools/STAR/STAR-Index.cwl chr1-star-index.yaml
  72 ```
  73
  74
  75 {% include links.md %}