setup.md

   1 ---
   2 title: Setup
   3 ---
   4
   5 <div>
   6 {% tabs setup %}
   7 {% tab setup generic %}
   8
   9 # Setting up a practice repository
  10
  11 We will create a new git repository and import a library of existing
  12 tool definitions that will help us build our workflow.
  13
  14 Create a new empty git repository to hold our workflow with this command:
  15
  16 ```
  17 git init rnaseq-cwl-training-exercises
  18 ```
  19 {: .language-bash }
  20
  21 Next, import bio-cwl-tools with this command:
  22
  23 ```
  24 git submodule add https://github.com/common-workflow-library/bio-cwl-tools.git
  25 ```
  26 {: .language-bash }
  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.jutro.arvadosapi.com/c=9178fe1b80a08a422dbe02adfd439764+925/
  36 ```
  37 {: .language-bash }
  38
  39 # Downloading or generating STAR index
  40
  41 Running STAR requires index files generated from the reference.
  42
  43 This is a rather large download (4 GB).  Depending on your bandwidth, it may be faster to generate it yourself.
  44
  45 ## Downloading
  46
  47 ```
  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/
  51 ```
  52 {: .language-bash }
  53
  54 ## Generating
  55
  56 Create `chr1-star-index.yaml`:
  57
  58 ```
  59 InputFiles:
  60   - class: File
  61     location: rnaseq/reference_data/chr1.fa
  62     format: http://edamontology.org/format_1930
  63 IndexName: 'hg19-chr1-STAR-index'
  64 Gtf:
  65   class: File
  66   location: rnaseq/reference_data/chr1-hg19_genes.gtf
  67 Overhang: 99
  68 ```
  69 {: .language-yaml }
  70
  71 Generate the index with your local cwl-runner.
  72
  73 ```
  74 cwl-runner bio-cwl-tools/STAR/STAR-Index.cwl chr1-star-index.yaml
  75 ```
  76 {: .language-bash }
  77
  78
  79 {% endtab %}
  80
  81 {% tab setup arvados %}
  82
  83 # Setting up a practice repository
  84
  85 We will create a new git repository and import a library of existing
  86 tool definitions that will help us build our workflow.
  87
  88 When using the recommended VSCode environment to develop on Arvados, start by forking this repository:
  89 ```
  90 git clone https://github.com/arvados/arvados-vscode-cwl-template.git rnaseq-cwl-training-exercises
  91 ```
  92 {: .language-bash }
  93
  94 Next, import bio-cwl-tools with this command:
  95
  96 ```
  97 git submodule add https://github.com/common-workflow-library/bio-cwl-tools.git
  98 ```
  99 {: .language-bash }
 100
 101 # Downloading sample and reference data
 102
 103 > ## Note
 104 >
 105 > You may already have access to this collection.
 106 >
 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.
 111 {: .callout}
 112
 113 Use `arv-copy` to copy the collection:
 114
 115 ```
 116 arv-copy --src jutro 9178fe1b80a08a422dbe02adfd439764+925
 117 ```
 118 {: .language-bash }
 119
 120 # Downloading or generating STAR index
 121
 122 Running STAR requires index files generated from the reference.
 123
 124 This is a rather large download (4 GB).  Depending on your bandwidth, it may be faster to generate it yourself.
 125
 126 ## Downloading
 127
 128 > ## Note
 129 >
 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.
 133 {: .callout}
 134
 135 Use `arv-copy` to copy the collection:
 136
 137 ```
 138 arv-copy --src jutro 02a12ce9e2707610991bd29d38796b57+2912
 139 ```
 140 {: .language-bash }
 141
 142 ## Generating
 143
 144 Create `chr1-star-index.yaml`:
 145
 146 ```
 147 InputFiles:
 148   - class: File
 149     location: keep:9178fe1b80a08a422dbe02adfd439764+925/reference_data/chr1.fa
 150     format: http://edamontology.org/format_1930
 151 IndexName: 'hg19-chr1-STAR-index'
 152 Gtf:
 153   class: File
 154   location: keep:9178fe1b80a08a422dbe02adfd439764+925/reference_data/chr1-hg19_genes.gtf
 155 Overhang: 99
 156 ```
 157 {: .language-yaml }
 158
 159 Generate the index with arvados-cwl-runner.
 160
 161 ```
 162 arvados-cwl-runner bio-cwl-tools/STAR/STAR-Index.cwl chr1-star-index.yaml
 163 ```
 164 {: .language-bash }
 165
 166 ## Sneak peak
 167 If you want to jump ahead, here are links to some of the CWL concepts you just used
 168   - [YAML array] (https://www.commonwl.org/user_guide/yaml/#arrays)
 169   - [CWL array inputs] (https://www.commonwl.org/user_guide/09-array-inputs/index.html)
 170
 171 {% endtab %}
 172 {% endtabs %}
 173 </div>
 174
 175 {% include links.md %}